Kanto: Misty. First off, she trains Water-types, which I absolutely adore. Second, she's a tomboy and tough girl in the games without being butch, which I find to be admirable. Third, okay, yeah, she was, for a long time, my second favorite anime character. Until she got the soul leech Togepi.
Johto: I've always been fond of Bugsy for the way he was portrayed in the anime as being a bit eccentric but clever. That and the countless assumptions that he was a girl in certain manga and by fans at the time = amusing.
Hoenn: Liza and Tate. Partly for the creepy factor in the games and partly because the anime made me like Tate. (Poor guy, always being cast in the shadow by his sister.)
Wallace is a close second, however, not only because of the Water-types but also because of the fruity artist vibe he emits.
Sinnoh: Literally no preference. Not even Crasher Wake here. Sorry, but none of the Gym Leaders in this generation strike me as interesting... or, well, normal. (Seriously, who was the character developer in this gen, and can I be on whatever he was on?) I might change this opinion if I actually watched the anime instead of just attempting to go off the games, but I really can't be arsed to sit in front of a television for long periods of time anymore. (Computer's a different story, though.)