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Yeah, Wes and Michael are missing from that list too from instance even if they aren't from Game Freak games. =p Wes I like the most as he's the most interesting of the bunch - the rest would be Gold and then Red for looks/nostalgia/in Red's case he's the only one to turn up in another game. Otherwise it's really just a case of looks imo, as there's no backstory or character to judge on if you only look on the surface (instead of say the manga or whatnot I suppose).
I loved playing with him and I'd love to see him reapear somewhere again Q.Q
After him I suppose I'd pick May :3 Though I also like Red due to references to Ash~
I'm partial to Kris. I like her in the manga, and I have nostalgia of playing Crystal. It was the first game you could play as a female, and I just liked her design. I have lots of fond memories playing as her.