(I'm not bumping, am I?)
My favorite Genesis game would be Sonic 3 and Knuckles.
I like Sonic 1, it's just not my favorite. Sonic 2 was really good.
But Sonic 3 and Knuckles was great. The savestates introduced in 3 were awesome. But the levels themselves. They seemed to be lengthened, and harder. Maybe they just seem longer because of the set up (Miniboss, act over, continue path)...
To me, it seemed the first game with an actual bit of storyline, which set up the rest of the series. Sure, in Sonic 1 and 2 you had to collect the emeralds and whatnot, but it didn't explain much.
This told us about the ME and Knuckles and all that.
Now, there were the Super Emeralds... But I'm just going to ignore that point right now. XD