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bear in mind that I don't play Pokemon competitively, so my favorites are based on appearance and my personal experience with it. (thus the reason of many Mega Evos and legendary Pokemons in the list)
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Bug
Genesect - cyborg bug transformer legendary = I WANT ONE
Yanmega - I love how it's based on the huge prehistoric dragonflies that once roamed the earth, makes it so much more cooler than butterflies and moths.
Shedinja - it's unique appearance and mythos backed up with Wonder Guard makes it quite the unique Pokemon I was looking for when I first played Emerald.

Dark
Mega Sableye - Sableye has always been my favorite Pokemon, but I just love how little GameFreak changed when they come up with a Mega Evo for it, it still retains the mischievous grin on its face.
Spiritomb - it's a spirit entrapped in a stone, and it has NO WEAKNESSES, pretty cool to be honest.
Yvetal - two words: OBLIVION WING. YES.

Dragon
Mega Rayquaza - I was originally going for the shiny version, but I think I'm used to the good old gigantic green dragon of the skies with yellow appendages sticking out, which somehow made it even more awesome.
Giratina Origin Form - I think the alternative form was quite derpy, but after I've watched the movie which it's original form and Shaymin starred in, its slick design won my heart over the fan favorite Charizard.
Mega Charizard X - who actually chose Mega Charizard Y over X? It's a black dragon with blue flames spilling out of its jaw, AND IT'S ACTUALLY A DRAGON TYPE.

Grass
Serperior - my go-to starter in Black, White, Black 2 and White 2. GIGA DRAIN FOR DAYS.
Torterra - also my go-to starter in Diamond, Pearl and Platinum, Torterra is actually the first Pokemon that I'd raised to level 100.
Lilygant - basically grass type Gardevoir and looking much cuter with its beady little eyes.

Ground
Zygarde - Pokemon of order, ORDER. How much more of a badass you can be with that title? Also I love the hexagon scales on its absence in the Pokemon XY story, it makes Zygarde seems more mysterious.
Shiny Primal Goudon - shiny regular Groudon? Gold, pretty awesome. Primal Groudon? Even more awesome. SHINY Primal Groudon? Another black dragon, and I LOVE black dragons.
Garchomp - its wings can fold up to make it resemble a jet, and it's a land shark Pokemon, it's a JET-LAND-SHARK-DRAGON.

Ice
Regice - my overall love for robotic stuff combined with its cry and death animation in Pokemon Battle Royal makes it my earlier favorites when I first got into Pokemon.
Froslass - another Gardevoir-like Pokemon, I just love her design...it's like a ghost-ice maiden in those folklore you heard passed down from older generations.
Black Kyurem - not exactly a black dragon, but I can look pass it with it GENERATOR tail and the wires that attached to it.

Electric
Heat Rotom - OMG IT'S SO CUTE I WANT ONE!!!!1!1!!!
Zekrom - more black dragons...but this one has a generator tail and an awesome cry.
Electivire - small touches like its double wire tail really makes it stand out from the rest of the electric Pokemon types.

Fairy
Shiny Mega Gardevoir - SHE WEARS BLACK NOW? WHAAAAAAAA-?
Shiny Xerneas - honestly I prefer the different shades of blue rather than the color spectacle that is regular Xerneas.
Mega Diancie - I love how its "dress" is made from jewels and gems, I might just have to make a card from it (hint hint)

Fighting
Meloetta Pirouette Form - JIGGLYPUFF EAT YOUR HEART OUT
Scrafty - officially known as the thug Pokemon complete with baggy pants and a Mohawk. Pokemon, for all ages indeed.
Mega Lucario - the only problem I have with it is that the appendages sticking out from its back head has no relationship with Giratina Origin Form. Make it happen GameFreak.

Normal
Arceus - god of all Pokemons, 'nuff said.
Regigigas - aside from the previously mentioned of my love for robotic beings, have you listened to its battle theme and cry?
Porygon-Z - also an artificial being, it's this weird twist on Pokemon that really draws me back to the franchise time after time.

Poison
Gengar - why not Mega Gengar? well it looks...unfitting to say the least. I love Gengar because of it's shadow copy abilities and it's an all around trouble maker.
Scollipede - BADASS GIGANTIC POISON SPITTING BALL ROLLING RED HOT CENTIPEDE. OH. MY. GOD.
Dragalge - BADASS GIGANTIC POISON SPITTING PURPLE LEAFY SEA ALGAE DRAGON. JESUS. CHRIST.

Psychic
Deoxys Defense Form - yes your precious Mewtwo is not number one, CRY FOR IT. I love Deoxys cause it's an alien virus, from a meteorite, and it battles Rayquaza, and its Defense Form looks like the Hulkbuster armor.
Mewtwo - yes, the original badass is here, but I can't put it any higher because it doesn't really have any impact on the story line in the past few generations.
Wobuffet - I watched the 3rd Gen Pokemon anime a lot, and Wobuffet is a big part of it. It may seem to be useless and a stupid Pokemon, but when it fights, god damn he's a TANK.

Fire
Mega Blaziken - my first Mega Evolution ever, and when it was first revealed in the Koro Koro magazine, I am stunned by how awesome Blaziken now looks.
Heatran - hands down my favorite fire type legendary Pokemon. This wall-crawling volcanic Pokemon has a sweet spot in my heart for having a very unique design.
Darmanitan Standard Mode - another trouble maker, mischievous looking Pokemon. Its design suits its personality so dam well it's uncanny.

Flying
Swellow - badass bird Pokemon which also coincidentally doubles as my go-to flying Pokemon every time I play the 3rd Gen games.
Lugia - Lugia is such a beast in the Pokemon 2000 movie, I have to put it in as my second favorite flying type Pokemon.
Honchkrow - gentleman, here's your equally classy dark crow Pokemon completed with a black fedora and classy suit like feathers.

Ghost
Chandelure - I can't keep my eyes off this Pokemon, the burning chandelier just keeps drawing me in.
Honedge - it actually surprises me how long it took GameFreak to make a sword Pokemon, but I'm glad they did. Better late than never.
Cofagrigus - living sarcophagus with eyes and sharp teeth? AND WITH SHADOW-Y ARMS COMING OUT OF ITS BODY? BADASS.

Rock
Cradily - prehistoric giant plant-cradle-lily thing ftw.
Gigalith - HUGE ROCK MONSTER IS FLIPPING AMAZING, YOU CAN'T DENY THAT.
Rampardos - I am a huge sucker for dinosaurs and with this Pokemon based off from the Pachycephalosauridae (can't even pronounce that correctly), my inner 7 year old just burst out with joy.

Steel
Mega Mawile - two heads are better than one. TWO HUGE JAWS ATTACH TO YOUR HEAD IS BETTER THAN ONE.
Magnezone - floating magnetic UFO thingy that can also use electric attacks...I NEED ONE FOR LIFE.
Shiny Metagross - a blue tank? Pretty amazing. A silver tank? Mind blowing-ly amazing. A silver tank with a GOLD CROSS? TAKE MY MONEY WILL YA GAMEFREAK.

Water
Wailord - herp derp biggest Pokemon in existence while also looking really cute and stuff.
Shiny Primal Kyogre - another black Pokemon! But this time it's a WHALE. Mind=Blown
Greninja - hands down, my favorite fighter to use in the new Smash Bros game.

Description
Blank by

bear in mind that I don't play Pokemon competitively, so my favorites are based on appearance and my personal experience with it. (thus the reason of many Mega Evos and legendary Pokemons in the list)
---------------------------------------------------------------------------
Bug
Genesect - cyborg bug transformer legendary = I WANT ONE
Yanmega - I love how it's based on the huge prehistoric dragonflies that once roamed the earth, makes it so much more cooler than butterflies and moths.
Shedinja - it's unique appearance and mythos backed up with Wonder Guard makes it quite the unique Pokemon I was looking for when I first played Emerald.

Dark
Mega Sableye - Sableye has always been my favorite Pokemon, but I just love how little GameFreak changed when they come up with a Mega Evo for it, it still retains the mischievous grin on its face.
Spiritomb - it's a spirit entrapped in a stone, and it has NO WEAKNESSES, pretty cool to be honest.
Yvetal - two words: OBLIVION WING. YES.

Dragon
Mega Rayquaza - I was originally going for the shiny version, but I think I'm used to the good old gigantic green dragon of the skies with yellow appendages sticking out, which somehow made it even more awesome.
Giratina Origin Form - I think the alternative form was quite derpy, but after I've watched the movie which it's original form and Shaymin starred in, its slick design won my heart over the fan favorite Charizard.
Mega Charizard X - who actually chose Mega Charizard Y over X? It's a black dragon with blue flames spilling out of its jaw, AND IT'S ACTUALLY A DRAGON TYPE.

Grass
Serperior - my go-to starter in Black, White, Black 2 and White 2. GIGA DRAIN FOR DAYS.
Torterra - also my go-to starter in Diamond, Pearl and Platinum, Torterra is actually the first Pokemon that I'd raised to level 100.
Lilygant - basically grass type Gardevoir and looking much cuter with its beady little eyes.

Ground
Zygarde - Pokemon of order, ORDER. How much more of a badass you can be with that title? Also I love the hexagon scales on its absence in the Pokemon XY story, it makes Zygarde seems more mysterious.
Shiny Primal Goudon - shiny regular Groudon? Gold, pretty awesome. Primal Groudon? Even more awesome. SHINY Primal Groudon? Another black dragon, and I LOVE black dragons.
Garchomp - its wings can fold up to make it resemble a jet, and it's a land shark Pokemon, it's a JET-LAND-SHARK-DRAGON.

Ice
Regice - my overall love for robotic stuff combined with its cry and death animation in Pokemon Battle Royal makes it my earlier favorites when I first got into Pokemon.
Froslass - another Gardevoir-like Pokemon, I just love her design...it's like a ghost-ice maiden in those folklore you heard passed down from older generations.
Black Kyurem - not exactly a black dragon, but I can look pass it with it GENERATOR tail and the wires that attached to it.

Electric
Heat Rotom - OMG IT'S SO CUTE I WANT ONE!!!!1!1!!!
Zekrom - more black dragons...but this one has a generator tail and an awesome cry.
Electivire - small touches like its double wire tail really makes it stand out from the rest of the electric Pokemon types.

Fairy
Shiny Mega Gardevoir - SHE WEARS BLACK NOW? WHAAAAAAAA-?
Shiny Xerneas - honestly I prefer the different shades of blue rather than the color spectacle that is regular Xerneas.
Mega Diancie - I love how its "dress" is made from jewels and gems, I might just have to make a card from it (hint hint)

Fighting
Meloetta Pirouette Form - JIGGLYPUFF EAT YOUR HEART OUT
Scrafty - officially known as the thug Pokemon complete with baggy pants and a Mohawk. Pokemon, for all ages indeed.
Mega Lucario - the only problem I have with it is that the appendages sticking out from its back head has no relationship with Giratina Origin Form. Make it happen GameFreak.

Normal
Arceus - god of all Pokemons, 'nuff said.
Regigigas - aside from the previously mentioned of my love for robotic beings, have you listened to its battle theme and cry?
Porygon-Z - also an artificial being, it's this weird twist on Pokemon that really draws me back to the franchise time after time.

Poison
Gengar - why not Mega Gengar? well it looks...unfitting to say the least. I love Gengar because of it's shadow copy abilities and it's an all around trouble maker.
Scollipede - BADASS GIGANTIC POISON SPITTING BALL ROLLING RED HOT CENTIPEDE. OH. MY. GOD.
Dragalge - BADASS GIGANTIC POISON SPITTING PURPLE LEAFY SEA ALGAE DRAGON. JESUS. CHRIST.

Psychic
Deoxys Defense Form - yes your precious Mewtwo is not number one, CRY FOR IT. I love Deoxys cause it's an alien virus, from a meteorite, and it battles Rayquaza, and its Defense Form looks like the Hulkbuster armor.
Mewtwo - yes, the original badass is here, but I can't put it any higher because it doesn't really have any impact on the story line in the past few generations.
Wobuffet - I watched the 3rd Gen Pokemon anime a lot, and Wobuffet is a big part of it. It may seem to be useless and a stupid Pokemon, but when it fights, god damn he's a TANK.

Fire
Mega Blaziken - my first Mega Evolution ever, and when it was first revealed in the Koro Koro magazine, I am stunned by how awesome Blaziken now looks.
Heatran - hands down my favorite fire type legendary Pokemon. This wall-crawling volcanic Pokemon has a sweet spot in my heart for having a very unique design.
Darmanitan Standard Mode - another trouble maker, mischievous looking Pokemon. Its design suits its personality so dam well it's uncanny.

Flying
Swellow - badass bird Pokemon which also coincidentally doubles as my go-to flying Pokemon every time I play the 3rd Gen games.
Lugia - Lugia is such a beast in the Pokemon 2000 movie, I have to put it in as my second favorite flying type Pokemon.
Honchkrow - gentleman, here's your equally classy dark crow Pokemon completed with a black fedora and classy suit like feathers.

Ghost
Chandelure - I can't keep my eyes off this Pokemon, the burning chandelier just keeps drawing me in.
Honedge - it actually surprises me how long it took GameFreak to make a sword Pokemon, but I'm glad they did. Better late than never.
Cofagrigus - living sarcophagus with eyes and sharp teeth? AND WITH SHADOW-Y ARMS COMING OUT OF ITS BODY? BADASS.

Rock
Cradily - prehistoric giant plant-cradle-lily thing ftw.
Gigalith - HUGE ROCK MONSTER IS FLIPPING AMAZING, YOU CAN'T DENY THAT.
Rampardos - I am a huge sucker for dinosaurs and with this Pokemon based off from the Pachycephalosauridae (can't even pronounce that correctly), my inner 7 year old just burst out with joy.

Steel
Mega Mawile - two heads are better than one. TWO HUGE JAWS ATTACH TO YOUR HEAD IS BETTER THAN ONE.
Magnezone - floating magnetic UFO thingy that can also use electric attacks...I NEED ONE FOR LIFE.
Shiny Metagross - a blue tank? Pretty amazing. A silver tank? Mind blowing-ly amazing. A silver tank with a GOLD CROSS? TAKE MY MONEY WILL YA GAMEFREAK.

Water
Wailord - herp derp biggest Pokemon in existence while also looking really cute and stuff.
Shiny Primal Kyogre - another black Pokemon! But this time it's a WHALE. Mind=Blown
Greninja - hands down, my favorite fighter to use in the new Smash Bros game.