based on favourite Pokemon solely:
Kanto: Squirtle
Johto: Heracross/Noctowl
Hoenn: Torkoal
Sinnoh: Torterra
Unova: Oshawott
Now, actually taking the Pokemon's personalities into account.
Kanto: Pikachu/Squirtle - Pikachu because obviously it pretty much has the most personality and I actually like it's personality too. Squirtle's a badass. Bulbasaur's good too though. Charizard was an *******...that's all I'm gonna say. He got better, sure, but at the time, no.
Johto: I'm gonna say Totodile, such a happy fellow. I really like the episode where he fell in love with an Azumarill and in the end, after getting dumped, instantly got over it after spotting a seemingly good looking female Quagsire. xD Like a Pokemon version of Brock...Really though Toto, a Quagsire? Seriously? Fine.
Hoenn: This one's kinda hard as all of his Pokemon had pretty good and unique personalities at this point. The sheer fact of Torkoal being my favourite Pokemon makes me love him no matter what. And I do like Ash's Torkoal, it was very emotional and a helpful guy as shown when it jumped into water to search for Spoinks pearl...and proceeded to sink due to being unable to swim...fun times.
Sinnoh: Since he's my second favourite Pokemon after Torkoal, I want to say Torterra. I really do. As a Turtwig and to a slightly lesser extent, Grotle it had some good personality and development. As a Torterra it sadly didn't get enough time to really do anything with Infernape and Dawn taking all the remaining time. And yes, Infernape had a ton of development and coolness to it. Ash's other Sinnoh pokes were good too but I'm gonna make it a tie between these two for Napes undeniable greatness and Turtwig/Grotle actually being important.
Unova: Oshawott. 'Nuff said. It's obvious that this guy's gonna be the new "Charizard" of Ash's team and I really like his character too.