I haven't played either games in a while, and I didn't finish colosseum, so this will be XD biased.
Obviously Miror B. The awesome trainer with a crazy fro, great music, and in XD he basically saved you whenever you missed a pokemon, and he he had Dragonite! He could be a fine neutral character again, if there were ever a sequel.
I suppose Gorigan (and Dakim) for being apes, and I liked the shadow pokemon Gorigan offered.
Greevil's great simply because he had a whole party of incredible Kanto pokemon.
I also have to respect normal Cipher grunts and other NPCs for their names alone.
Also, Colosseum's generic characters are hilarious (looking), especially the female bodybuilder and the male bodybuilder who I picture when I think of Axl Rose (dunno why).
Chobin too, for his hilarious support of Kaminko.
All in all, they really capitalized on the opportunity to make unique characters in the games.