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Description
The science and practice of organizing and classifying Pokémon into a coherent ordering that does not directly contradict the already well-established taxonomy of all other life forms is a daunting task that has troubled Pokémon biologists for some time due to several main factors: the general differences between Pokémon and other life forms at the cellular level; contrary to that, the similarities in body structure of many Pokémon and similar animals; the dilemma of whether to count Pokémon as more closely related by Elemental type or by body structure; and the lack of any sort of clear pattern of common decent amongst Pokémon, contrary to most other categories of life.

The first and foremost point that must be addressed in Pokémon Biology is their inherent cellular energy signature.  This is the reason why Pokémon's cell structure can be easily destabilized and compressed into energy for storing inside a Poké ball.  It is also the reason why Pokémon evolve—rather than undergoing a gradual process of maturity like ordinary plants and animals, their energy signature changes at once from a stimulus, be it an increase in strength, radiation from an Elemental Stone, or a certain emotional state.  This fluctuation triggers the genome for their evolved form and starts a sudden change in body structure.  (It is, of course, important to recognize Pokémon evolution as a metamorphosis completely unrelated to the principle of evolutionary descent.  Also of note is the fact that this process is separate from sexual maturity, as the vast majority of Pokémon do not need to reach a higher evolutionary level in order to reproduce.)

A family is a self-contained evolutionary line of Pokémon.  Each individual Pokémon has a unique energy signature, much like each life form has a unique genetic code—similarities that determine how closely related a Pokémon is to others are determined by species, element, and type.

Upper Classification Split

There is relatively little debate that Pokémon fit into the Domain of Eukarya.  The fact that their cell structure is distinctly different from other life forms was originally a cause for concern, but it is agreed upon that this difference is generally on the same level as the cell difference between plants and animals.  This, however, requires that Pokémon be placed in a separate Kingdom of Pokémonia.

The trouble is that Pokémon share many of the classifying characteristics and body structures of Animals and Plants, requiring a split in the traditional taxonomic setup.  Pokémon can be sorted into Sub-kingdoms of Animalia, Plantae, and Umbrae (gaseous or spirit-like Pokémon, or those with amorphous bodies ).  It is important to note that even Pokémon that may be sorted into a Sub-kingdom other than Animalia generally have many similarities with animals, often being heterotrophs to a certain degree alongside photosynthesis or other feeding methods, and by being motile.

Energy signature classification is fairly simple, being based solely on the Pokémon's Elemental Type, and further categorized into subtypes within each Element (for Elements that have subtypes).

The Elemental Conundrum

For the longest time, the only concrete method of organizing Pokémon taxonomically was by Element, as ever since technology allowed for easy harnessing of Pokémon energy, it has been quite simple to analyze the variations in different Pokémon's energy signatures.  Even before this breakthrough, Pokémon Elemental types are easily observed.  There is a definite relationship between Pokémon of the same Element, but how does this compare with similarities in body structure, and what really is the "right" way to categorize Pokémon relations?

It has long been accepted that different body structures in Pokémon arose separately from different Elements, as there is little correlation between the two.  For example, a Pokémon that resembles an animal in the reptile family may have any number of different Elements, but a Pokémon that is similar to a mammal could have them just the same.  It is now theorized that somewhere very early in Pokémon development, the creatures' cell structure deviated towards being energy based and capable of being destabilized.  This would be considered a "neutral" element that does not exist today.  After Pokémon had already diversified in body form, the neutral energy structure reached a level that made it highly susceptible to outside influence, either from environmental factors or from the rich energy in the earth throughout certain regions that Pokémon first inhabited.  These energies within the earth are now thought to be the origin of Elemental Stones.  A combination of environmental pressures and reactions with outside energies caused Pokémon to pick up elemental traits.  Depending on the particular area or situation, a wide variety of Pokémon could develop the same Element despite not being closely related.  This is the reason why Pokémon whose DNA is rather dissimilar may in fact have very similar energy signatures.

The Normal type is the closest modern link to the neutral element (but it itself is clearly not neutral, as Normal-type Pokémon are often capable of learning a wide range of elemental moves).  Eevee is the only living Pokémon to be very close to a neutral element (as evidenced by its highly reactive energy signature.)

It has recently been proposed that Elements be incorporated into the newly categorized Breeding Group system, as it is a more specific trait (as such, it is located near the bottom of a complete taxonomic ordering, just above family-species.)

Differences from Traditional Classification

While other life forms are sorted by their degree of relation to other species, it is largely impossible to do that with Pokémon due mainly to the unique fact that Pokémon can breed with other species within a wide range known as a breeding group.  This is clearly the most distinct and definite observable pattern of relationships amongst Pokémon species, as it forms a rough guideline for patterns of body type, as well as the obvious reproductive compatibility that links Pokémon of similar physical structure.

Pokémon biologists must remember that Pokémon can be capable of breeding within two breeding groups, either by being close to the "branch" of two groups, or by having developmentally converged towards a second group.  There are many branches in Pokémon development that join back together—this is a very major difference from animals.  For example, Wailmer, despite being mammalian (and in the ground group), can breed with other water-group Pokémon of similar body structure to it, even though they are fish.

Notes:

The indeterminate group is mostly comprised of umbra Pokémon, but there are a few animalian Pokémon such as the Slugma and Ralts lines.  They are the closest link between the two sub-kingdoms.  Even when umbra Pokémon diverged from the animalian line, they retained the ability to breed with those in their group.

Baby Pokémon and Pokémon incapable of breeding should be classified according to the other species in their family, if any.

Scientists have concluded that Unown reproduce in a method vastly different from other Pokémon, and cannot and/or will not do so when captured.  No details on the true method have been observed, however, so no efforts to duplicate this effect can been made, by either trainers or researchers.  The Pokémon is essentially non-breedable, but until further notice, shall be classified as Indeterminate due to some DNA similarities.

The only other Pokémon that have no recorded breeding capabilities are Legendary Pokémon.  For the Legendaries who are presumed non-unique, it is believed that they only reproduce with others of their own species, (though even this is enigmatic, as the sex of most Legendaries is impossible to determine.  Even chromosomal analysis on DNA samples yields no conclusive evidence.)

For Legendaries that are, in fact, believed to be one-of-a-kind, some manner of asexual reproduction or rebirth may take place.  All Legendaries exhibit a unique fluctuation in energy structure that developed long before most Elemental-type distinctions had been made.  For this reason, all Legendaries, unique or not, are placed into the group Aethereus.

Ground – Terramammus
Monster – Belluae
Dragon – Anguis
Flying – Volatus
Fairy – Tenerrimus
Humanshape – Hominiformes
Bug – Bestiolae
Water1 – Aquatilis
Water2 – Piscis
Water3 – Sineosseus
Plant – Herbae
Mineral – Minerales
Indeterminate – Amorphes
Nonbreeding – Aethereus

Elemental Connections

Again, it must be stressed that for the majority of Pokémon, there is little to no connection between body type and energy signature.  The two factors are almost universally agreed to have arisen separately.  However, there are certain exceptions where body type did in fact influence what Element a Pokémon gained, which shall be addressed here.

Dragon
There is a high correlation between Pokémon in the Dragon breeding group and Pokémon that are Dragon-type.  As Pokémon with a draconian body structure began to branch out, the Dragon-type energy structure became linked to it.

Bug
There is a high correlation between Pokémon in the Bug breeding group and Pokémon that are Bug-type.  Similarly to dragons, the bug element arose in Pokémon whose bodies were structured most similarly to animal arthropods and insects.

Flying
All Pokémon in the flying breeding group are Flying-types.  The Flying element obviously arose through flight, even in the cases of flightless Pokémon closely related to other flying Pokémon (like Doduo.)  This is why even Pokémon not remotely related to flying-group Pokémon (like Charizard) still exhibit the Element.  Not all flight-capable Pokémon would develop the Element, however, if another influence was stronger (such as with Flygon.)

Water
Almost all Water-type Pokémon are related to one of the three water breeding groups.  It is clear that an aquatic lifestyle influenced the development of the Water Element.

Grass
All plant-division Grass-types are in the plant breeding group.  This split in the way Grass types are sorted is much higher in the taxonomic order than Elemental sub-types, and should be regarded as more significant.  Animalian Grass-type Pokémon might have gained their element through specific regional/environmental pressures, coupled with certain types of energy-based plant-life in the Pokémon regions, allowing their bodies to symbiotically grow vegetation with the same energy type that the plant-division Grass-types developed.  This is one of the only examples of convergent evolution within an Element or breeding group.  The influence of the plant growth would allow animalian Grass-types to breed with plant-division ones.

There are several more minor connections, such as a slight correlation between Ghost-types and the indeterminate breeding group, for example.  However, it must be noted this factor does not oppose what is already known about Pokémon development.  It simply means that Pokémon with those body types were more predisposed to develop certain elemental traits (for example, the Flying Element obviously had a tendency to develop in Pokémon capable of flight, but could still develop in other similar Pokémon just as well).  It does not mean that their Elements developed any differently than other Pokémon's.

A Complete Example

Presented here is a diagram of a relatively simple animalian Pokémon's full taxonomic classification.

Lucario:

Kingdom – Pokémonia
----- Sub-kingdom – Animalia
Group – Terramammus
----- Sub-group – Hominiformes
Element – Combatamechana
----- Sub-type – Adamasinteri
Family – Etherus
Species – Sentire

Some important notes to keep in mind:

Lucario's Elemental sub-type is presented because Steel-types are very clearly classified into two groups: internal and external (depending on whether they exhibit a metallic hide/appendages, or a metallic skeleton).  Not all types have such distinctions.  And in the case of some types (such as Electric), there are several overlapping subdivisions.  For this reason, Pokémon biologists need not specify sub-type distinctions in their scientific papers if they do not wish to.  Such a task is best left to type experts.

Pokémon within the same evolutionary family obviously share the same family name, but some closely related Pokémon lines will share the same family name.  There is some dispute amongst Pokémon biologists over whether the family name should be restricted to evolutionary families, and a new taxonomic level be used to sort closely related Pokémon families.  However, the aforementioned problem of breeding groups makes it difficult to determine how closely related two lines of Pokémon are, since Pokémon cannot be sorted into clades like animals can.

Use of either a Pokémon's binomial or trinomial name in scientific use has come down to personal preference.  The individual Element names have already been categorized and are generally well-known.  Many Pokémon have not been sorted into family-species, however.  Pokémon biologists are encouraged to do so when researching a particular specimen.

Description
The science and practice of organizing and classifying Pokémon into a coherent ordering that does not directly contradict the already well-established taxonomy of all other life forms is a daunting task that has troubled Pokémon biologists for some time due to several main factors: the general differences between Pokémon and other life forms at the cellular level; contrary to that, the similarities in body structure of many Pokémon and similar animals; the dilemma of whether to count Pokémon as more closely related by Elemental type or by body structure; and the lack of any sort of clear pattern of common decent amongst Pokémon, contrary to most other categories of life.

The first and foremost point that must be addressed in Pokémon Biology is their inherent cellular energy signature.  This is the reason why Pokémon's cell structure can be easily destabilized and compressed into energy for storing inside a Poké ball.  It is also the reason why Pokémon evolve—rather than undergoing a gradual process of maturity like ordinary plants and animals, their energy signature changes at once from a stimulus, be it an increase in strength, radiation from an Elemental Stone, or a certain emotional state.  This fluctuation triggers the genome for their evolved form and starts a sudden change in body structure.  (It is, of course, important to recognize Pokémon evolution as a metamorphosis completely unrelated to the principle of evolutionary descent.  Also of note is the fact that this process is separate from sexual maturity, as the vast majority of Pokémon do not need to reach a higher evolutionary level in order to reproduce.)

A family is a self-contained evolutionary line of Pokémon.  Each individual Pokémon has a unique energy signature, much like each life form has a unique genetic code—similarities that determine how closely related a Pokémon is to others are determined by species, element, and type.

Upper Classification Split

There is relatively little debate that Pokémon fit into the Domain of Eukarya.  The fact that their cell structure is distinctly different from other life forms was originally a cause for concern, but it is agreed upon that this difference is generally on the same level as the cell difference between plants and animals.  This, however, requires that Pokémon be placed in a separate Kingdom of Pokémonia.

The trouble is that Pokémon share many of the classifying characteristics and body structures of Animals and Plants, requiring a split in the traditional taxonomic setup.  Pokémon can be sorted into Sub-kingdoms of Animalia, Plantae, and Umbrae (gaseous or spirit-like Pokémon, or those with amorphous bodies ).  It is important to note that even Pokémon that may be sorted into a Sub-kingdom other than Animalia generally have many similarities with animals, often being heterotrophs to a certain degree alongside photosynthesis or other feeding methods, and by being motile.

Energy signature classification is fairly simple, being based solely on the Pokémon's Elemental Type, and further categorized into subtypes within each Element (for Elements that have subtypes).

The Elemental Conundrum

For the longest time, the only concrete method of organizing Pokémon taxonomically was by Element, as ever since technology allowed for easy harnessing of Pokémon energy, it has been quite simple to analyze the variations in different Pokémon's energy signatures.  Even before this breakthrough, Pokémon Elemental types are easily observed.  There is a definite relationship between Pokémon of the same Element, but how does this compare with similarities in body structure, and what really is the "right" way to categorize Pokémon relations?

It has long been accepted that different body structures in Pokémon arose separately from different Elements, as there is little correlation between the two.  For example, a Pokémon that resembles an animal in the reptile family may have any number of different Elements, but a Pokémon that is similar to a mammal could have them just the same.  It is now theorized that somewhere very early in Pokémon development, the creatures' cell structure deviated towards being energy based and capable of being destabilized.  This would be considered a "neutral" element that does not exist today.  After Pokémon had already diversified in body form, the neutral energy structure reached a level that made it highly susceptible to outside influence, either from environmental factors or from the rich energy in the earth throughout certain regions that Pokémon first inhabited.  These energies within the earth are now thought to be the origin of Elemental Stones.  A combination of environmental pressures and reactions with outside energies caused Pokémon to pick up elemental traits.  Depending on the particular area or situation, a wide variety of Pokémon could develop the same Element despite not being closely related.  This is the reason why Pokémon whose DNA is rather dissimilar may in fact have very similar energy signatures.

The Normal type is the closest modern link to the neutral element (but it itself is clearly not neutral, as Normal-type Pokémon are often capable of learning a wide range of elemental moves).  Eevee is the only living Pokémon to be very close to a neutral element (as evidenced by its highly reactive energy signature.)

It has recently been proposed that Elements be incorporated into the newly categorized Breeding Group system, as it is a more specific trait (as such, it is located near the bottom of a complete taxonomic ordering, just above family-species.)

Differences from Traditional Classification

While other life forms are sorted by their degree of relation to other species, it is largely impossible to do that with Pokémon due mainly to the unique fact that Pokémon can breed with other species within a wide range known as a breeding group.  This is clearly the most distinct and definite observable pattern of relationships amongst Pokémon species, as it forms a rough guideline for patterns of body type, as well as the obvious reproductive compatibility that links Pokémon of similar physical structure.

Pokémon biologists must remember that Pokémon can be capable of breeding within two breeding groups, either by being close to the "branch" of two groups, or by having developmentally converged towards a second group.  There are many branches in Pokémon development that join back together—this is a very major difference from animals.  For example, Wailmer, despite being mammalian (and in the ground group), can breed with other water-group Pokémon of similar body structure to it, even though they are fish.

Notes:

The indeterminate group is mostly comprised of umbra Pokémon, but there are a few animalian Pokémon such as the Slugma and Ralts lines.  They are the closest link between the two sub-kingdoms.  Even when umbra Pokémon diverged from the animalian line, they retained the ability to breed with those in their group.

Baby Pokémon and Pokémon incapable of breeding should be classified according to the other species in their family, if any.

Scientists have concluded that Unown reproduce in a method vastly different from other Pokémon, and cannot and/or will not do so when captured.  No details on the true method have been observed, however, so no efforts to duplicate this effect can been made, by either trainers or researchers.  The Pokémon is essentially non-breedable, but until further notice, shall be classified as Indeterminate due to some DNA similarities.

The only other Pokémon that have no recorded breeding capabilities are Legendary Pokémon.  For the Legendaries who are presumed non-unique, it is believed that they only reproduce with others of their own species, (though even this is enigmatic, as the sex of most Legendaries is impossible to determine.  Even chromosomal analysis on DNA samples yields no conclusive evidence.)

For Legendaries that are, in fact, believed to be one-of-a-kind, some manner of asexual reproduction or rebirth may take place.  All Legendaries exhibit a unique fluctuation in energy structure that developed long before most Elemental-type distinctions had been made.  For this reason, all Legendaries, unique or not, are placed into the group Aethereus.

Ground – Terramammus
Monster – Belluae
Dragon – Anguis
Flying – Volatus
Fairy – Tenerrimus
Humanshape – Hominiformes
Bug – Bestiolae
Water1 – Aquatilis
Water2 – Piscis
Water3 – Sineosseus
Plant – Herbae
Mineral – Minerales
Indeterminate – Amorphes
Nonbreeding – Aethereus

Elemental Connections

Again, it must be stressed that for the majority of Pokémon, there is little to no connection between body type and energy signature.  The two factors are almost universally agreed to have arisen separately.  However, there are certain exceptions where body type did in fact influence what Element a Pokémon gained, which shall be addressed here.

Dragon
There is a high correlation between Pokémon in the Dragon breeding group and Pokémon that are Dragon-type.  As Pokémon with a draconian body structure began to branch out, the Dragon-type energy structure became linked to it.

Bug
There is a high correlation between Pokémon in the Bug breeding group and Pokémon that are Bug-type.  Similarly to dragons, the bug element arose in Pokémon whose bodies were structured most similarly to animal arthropods and insects.

Flying
All Pokémon in the flying breeding group are Flying-types.  The Flying element obviously arose through flight, even in the cases of flightless Pokémon closely related to other flying Pokémon (like Doduo.)  This is why even Pokémon not remotely related to flying-group Pokémon (like Charizard) still exhibit the Element.  Not all flight-capable Pokémon would develop the Element, however, if another influence was stronger (such as with Flygon.)

Water
Almost all Water-type Pokémon are related to one of the three water breeding groups.  It is clear that an aquatic lifestyle influenced the development of the Water Element.

Grass
All plant-division Grass-types are in the plant breeding group.  This split in the way Grass types are sorted is much higher in the taxonomic order than Elemental sub-types, and should be regarded as more significant.  Animalian Grass-type Pokémon might have gained their element through specific regional/environmental pressures, coupled with certain types of energy-based plant-life in the Pokémon regions, allowing their bodies to symbiotically grow vegetation with the same energy type that the plant-division Grass-types developed.  This is one of the only examples of convergent evolution within an Element or breeding group.  The influence of the plant growth would allow animalian Grass-types to breed with plant-division ones.

There are several more minor connections, such as a slight correlation between Ghost-types and the indeterminate breeding group, for example.  However, it must be noted this factor does not oppose what is already known about Pokémon development.  It simply means that Pokémon with those body types were more predisposed to develop certain elemental traits (for example, the Flying Element obviously had a tendency to develop in Pokémon capable of flight, but could still develop in other similar Pokémon just as well).  It does not mean that their Elements developed any differently than other Pokémon's.

A Complete Example

Presented here is a diagram of a relatively simple animalian Pokémon's full taxonomic classification.

Lucario:

Kingdom – Pokémonia
----- Sub-kingdom – Animalia
Group – Terramammus
----- Sub-group – Hominiformes
Element – Combatamechana
----- Sub-type – Adamasinteri
Family – Etherus
Species – Sentire

Some important notes to keep in mind:

Lucario's Elemental sub-type is presented because Steel-types are very clearly classified into two groups: internal and external (depending on whether they exhibit a metallic hide/appendages, or a metallic skeleton).  Not all types have such distinctions.  And in the case of some types (such as Electric), there are several overlapping subdivisions.  For this reason, Pokémon biologists need not specify sub-type distinctions in their scientific papers if they do not wish to.  Such a task is best left to type experts.

Pokémon within the same evolutionary family obviously share the same family name, but some closely related Pokémon lines will share the same family name.  There is some dispute amongst Pokémon biologists over whether the family name should be restricted to evolutionary families, and a new taxonomic level be used to sort closely related Pokémon families.  However, the aforementioned problem of breeding groups makes it difficult to determine how closely related two lines of Pokémon are, since Pokémon cannot be sorted into clades like animals can.

Use of either a Pokémon's binomial or trinomial name in scientific use has come down to personal preference.  The individual Element names have already been categorized and are generally well-known.  Many Pokémon have not been sorted into family-species, however.  Pokémon biologists are encouraged to do so when researching a particular specimen.