For me it has always been Sonic 2. The level design is just fantastic, I've been playing Sonic Rush on the DS recently and the amount of times I die through a pit fall is just unbearable. Sonic 2 offers a brilliant sense of speed that I can navigate with confidence - That isn't necessarily saying it is easy... it does offer a decent challenge but I find it is a game I enjoy to play more casually. There are a few things I dislike, the biggest being the bonus stages as they're really difficult - I much prefer Sonic 3's with the intensity of how fast it gets.
I think considering the difference between 2D Sonic & 3D Sonic, it is worth mention the latter too. For me it is Sonic Adventure 1... & I KNOW it is far from a perfect game
But I always really enjoyed the games structure, the open world segments felt fun and really gave a great presence to the world. Sonic Unleashed had these too of course but I guess I found all the sidequests with the people tedious. I also enjoyed the majority of the story and playing as other characters (Discounting BIG). Its a game I really had fun 100% completing, I got all the emblems and everything. The 2nd game just had all sorts of short comings which got in the way for me - Knuckles/Rogue Stages having the indicator locked making you have to find the treasure in order or Just how clunky the Tankbot felt in Tails/Robotnik missions.