1: Giovanni: The misfit, the man who threw away the honor and titles for a life of crime. His intellect with his money but his strength fed by his indominable will makes him worthy of his titles. He doesn't need the Rockets to prove himself, but they do need him. His complexity is the least of his true inner qualities.
2: Sabrina: the most mysterious along with the most powerful (second only to Giovanni) makes her runner up as favorite. Her power with her miserable past and her feared status makes her more than the cookie cutter "goth girl". But unlike the favorite archetype done by Teen Titans' Raven in that of she is allowed to overstep her bounds and be automatically excused for such actions, Sabrina knows of the great power that lies within and she knows about her roles and responsibilty to hopefully restrain herself, despite such extensions (her doll) of her powers.
3: Brock: One of the most horniest characters there is combined with the weirdest eyes ever, a man of character and empathy, and voiced by Eric Stuart? Need you ask?
4. Faulker: A pity there isn't more to the first Johto Gym Leader with his grand ambition: to fly like the birds. This with Nathan Price's excellent portrayal creates one of the more profound Gym Leaders.
5: Bugsy: The boy with the mop head, but one of an egg head as his scientific curiosity with insects and his own research makes him not only one of the more intellectual characters, but certainly one of the more fleshed out as his life is more than the game. Not to mention, he's also one of open minded ness, by choosing the Bug type, the downtrodden type (complete with a defensive/lecturing attitude about them) and expanding his mind. All this and adorable anime looks. He's a plushie essentially.
But those are my choices.