I've been meaning to do this, but I never got bored enough to do it. However, being sick at home today, I finally willed myself to do it.
So, through a long, tedious, boring process of narrowing down the field of 649, I have created a list of my top 5 favorite pokemon.

5. Infernape
  Reason: He's a fire monkey. Need I say more?
4. Zekrom
  Reason: I have liked Zekrom since he was first announced. He's a giant........something...with a generator for a tail. He's also a                      
  Dragon/Electric type, which is just an interesting combination to me.
3. Deoxys
  Reason: The first Pokemon Movie I watched was Destiny Deoxys (I guess technically it would be Mewtwo Strikes Back, but I was
  too little to understand what was happening) and ever since, Deoxys has been one of my favorites.
2. Charizard
  Reason: He's Charizard. The original beast. Why wouldn't he be on this list?
1. Blaziken
  Reason: It was tough deciding between Blaziken and Charizard, so here's the full argument to support Blaziken being number 1 on
  this list. I chose Blaziken mainly because I started playing Pokemon in Generation III. I'm not joking when I say that this giant fire
  chicken was my companion. I know it's just a game, and technically I didn't even raise him from the beginning (I got the game from a
  friend after he had beaten the first 3 gyms), but I raised him to level 100 with no help, being almost clueless about the game and
  how it was to be played. He was with me (that is, my trainer character) through everything. Blaziken was and is to me what
  Charizard or Pikachu is to everyone else. He's that one Pokemon that will always be linked with the fondest of memories, and he lives
  on through the Blaziken in my Black 2 version. Although it isn't the same one, each successor carries on the legacy of the original.