hard to decide... I'm highly inclined to love the original Holy Trinity of Sonic, Tails, and Knuckles. Sonic is pretty much the franchise itself, and I can't say he's had a bad personality since the transition to 3D (plus Jun'ichi Kanemaru's portrayal is awesome). Tails was friggin' fun to play as back in the Genesis days, and would easily qualify as my #1 choice, but in the 3D games, he's been doing a lot less ass-kicking directly and relying too much on his gadgets (not the least of which being those shitty, shitty ring bombs... this wouldn't be so bad if they'd have at least handled his genius more like Tails' Adventure did). Not only that, but any characterization he got over the Sonic Adventure games is pretty much wiped clean now and he's been reduced back to a mere sidekick who can't even be playable nowadays.
And Knuckles... he's alright, added variety to the now-legendary trio of playables back in the day, but personality-wise, the guy's gotta be as dumb as a doormat (though thankfully, I haven't seen him acting so friggin' gullible since Sonic Advanced 2). He served as an alright rival to Sonic for a while, but like Tails, his characterization has also suffered to a mere sidekick who doesn't even seem attached to Angel Island any longer. Also, treasure-hunting, need I say more? Come to think of it, his short jump was murder back in the Genesis days (I guess it was their excuse to not let Knuckles take the same paths as Sonic and Tails, but man, that made the final boss in Sonic 2 far more brutal, as if 0 rings wasn't bad enough). I guess I love the guy by default just for being one of the three classic main characters, but he's certainly my least favorite of the three.
Maybe I should just cop out and choose Metal Sonic like Chris did. He didn't really suffer much into the 3D era (personally, I don't think the Chaotix did either, not that they appeared often enough to begin with, but they're not on the poll). Come to think of it, Dr. Eggman's also still well and good (and was one of the only good parts of Sonic X) if you're willing to overlook his "try to awaken some ancient evil/lost technology/whatever and be overtaken by it" formula that plagued him for a few games.