Um, Sonic 3 alone fells like an unfinished game.... because it's an unfinished game. The last Launch Base level is not a proper final level, and the last boss is a joke. With Sonic & Knuckles attached, it surely feels as the epic complete game that Sonic 3 should have been from the beginning, had it not been for the greed of Sega when they split the game and sold it *twice*.
Thus, I refuse to consider Sonic3 and Sonic & Knuckles as two separate releases. With this in mind, my ranking about level design would be:
Sonic 3 & Knuckles > Sonic 2 >> Sonic 1 >> Sonic CD >>>>>>> Sonic Advance.
First of all, I agree that the Sonic Advance series cant' compare with the old games when it comes to gameplay, because it just consists of a senseless running and running.
Sonic 3 and Sonic 2 are very close, but Sonic 3 has the Knuckles paths and the game, despite featuring much larger levels, feels even more polished than the second one in all aspects. Even the Carnival Night Zone or that crazy last Death Egg zone made sense after some playing for me.
Sonic 1 is clearly below those two games, and Sonic CD is even lower IMO. Sonic CD feels like a bastard sequel/remake of Sonic 1, (bastard because the real sequel was the already released Sonic 2). The stages have too much abrupt edges and walls that break the flow of the gameplay, and some elements like the spindash are worse implemented than in Sonic 2. On the other hand, the game has probably the best soundtrack of any Sonic game, and some very inspiring visuals (artistic-wise), but when it comes to gameplay and level design it's clearly the worst of the 16-bit Sonic games IMO.