Oh man, I can't just choose one! My favorites are Morty, Jasmine, Pryce, and Misty.
Morty has always given off the air of cool and intelligent. I love his interest in the history of his city/region, and Ghost is an awesome type!
Jasmine is quiet and calm, yet very strong at the same time. And she has that bond with her Pokemon that you really saw in the anime and even slightly in the game (Ampharos).
Even though his gym was relatively easy, he is still one of my favorite gym leaders. He's cool and wise, and I really liked his character in the anime.
Finally, Misty. Probably only because she was one of my favorite characters in the anime, but also because I love water-types. I just wish they didn't give her that hideous outfit and hairdo in the game!