For some odd reasons, I tend to like those Legendary Pokemon rather then those common ones. They just have a sense of awesomeness. my favorite one ofcourse would be Arceus as he has Judgement!
Playing with the legendary pokemon almost feels like cheating sometimes. Nothing wrong with it essentially but you are getting a pokemon at level 60 or above who's always stronger than those of the same type and level. Mewtwo goes one step ahead and is even more powerful.
Definitely Salamence! Finding and training a Bagon reminded me of catching and leveling up a Dratini in the classic Pokemon Red.
I've always liked Scyther, he looked like a real badass. Never liked Scizor though, I think it's really a crappy evolution. But I'm only speaking about it's looks, not for gameplay. In games, I really liked Ghastly and Alakazam.
My favourite is either Arceus or Kyurem, I always like the strongest Pokemon. I can't decide which one is better though... I also like Dragon Type Pokemon and both are Dragon Type's so I'd say, I like them both.
My favorite Pokemon would have to be Squirtle. I've always loved Water Type Pokemon so when I first played Pokemon Blue, I instantly fell in love when I could choose Squirtle during the beginning of the game. I remember instead of going to the next town, I stayed at the grass near pallet town to train him and I got him to level 15! (Took me awhile though). I believe when Squirtle was level 16, he evolved into Wartortle and then Blastoise. One thing that I really liked about Blastoise were the two guns coming out of his shell. That really caught my eye right away.
My favorite type is Psychic so Alakazam is the Pokemon I like the most. Unlike most Pokemons, he looks so grim and disturbing. He is poweful but useful only in some battles.
I'm going to be old school and say Bulbasaur. I always choose leaf type as my starter and Bulbasaur was the first.
Good ol' #143 Snorlax. I'm partial to normal types, and I remember as a kid capturing Snorlax and he was so powerful. The first pseudo legendary in the game. Plus he's a sweet dude. Chill, he likes to eat and sleep. I can totally get behind that.
I loved Chikorita. When I had the gold version, she was always my favorite pick. I love her. I also tended to favor Chikorita because of the anime. I just always imagined her to be just like the anime version.
Having not spent too much time on previous Pokemon games, I'm playing X and I really like Fletchling. It wasn't the first Pokemon I latched onto, but it's quickly become my favorite as I'm playing and letting it evolve.
I really like Torterra, the idea of a massive turtle that's growing trees off of its back seems awesome to me.
I like Totodile, I think he's a pretty swell alligator with a swell personality I mean what's not to love about Feraligatr? Shuckle also a favorite but that just because he s the possibility to do the single highest damage in the game, he's a technical love for me. That and Magikarp, because a swift swim Magikarp with 1 HP flaying about, is something magical that only Magikarp can do.
My favorite pokemon would be the new generation starter Snivy. He just looks so cool and sly even though he's one of the worst starters stat-wise for me, (I hate speed).
I loved Blaziken, because it looked more like some sort of super hero, rather than a pokemon... plus its one of the more powerful fire types that isn't a legendary, and I love fire types...
Chikorita, partly because it was my first starter. Also, grass type is best type. That or the Bulbasaur evolutions. Leech Seed + Poison Powder + Take Down.
I would have to say Yanmega. Although I'm partial to any of the Generation 1/3 ghost Pokemon like Ghastley or Haunter.
I tend to like the final evolutions of all the fire type starter pokemon, so like: Charizard, Blaziken, Typlhosion, Ifernape and Emboar