Mine is a tie between 3 games:
Sonic 3 (and S3&K I guess): This is my favourite sonic game and what I consider the closest to a near-perfect sonic 2D game. The level design is awesome, because you go all around and not from left to right. Not that saying otherwise is a particularly bad thing. You know what's funny? I used to think that Sonic 2 was the best Sonic 2D game, but now I have played Sonic 3 & Knuckles, I think that's much better. I even prefer Sonic CD over 2. The reason I put (S3&K) in brackets is because I don't really enjoy the & Knuckles stages that much. Not that I loathe them, as I really like Lava Reef Zone, and Sandopolis is pretty cool.
Sonic Adventure 2: Aah, I really like this game. Mostly the Sonic stages, I still like the hunting stages though, they're ok. I like spin dashing through the levels, and the level layout. I actually don't hate any of the Sonic/Shadow stages and I adore the Chao Garden!!! Ahh the memories trying to get chaos chao and leaving the gamecube on overnight lol.
Sonic Heroes: This is my first sonic game ever, if you don't count Sonic 3D Blast 5 (The music is loud and terrible). I love all the levels, and to be honest I don't really hate playing the same stage 4 times, but I can see that being a problem. I like the how colourful the levels are and I found them really memorable to be honest. The bosses are one of the best in the series as well imo.