The music was a huge (HUGE) step down from Sonic 2. I don't understand the obsession over the music in S3&K, especially Ice Cap. I REALLY don't see what's so special about that zone's music, nor the rest of the game.
Its soundtrack will never, EVER reach the greatness that was Sonic 2's. Mystic Cave Zone? AMAZING. Chemical Plant Zone? ASTONISHING.
Knuckles was just the beginning of the shitty "throw random new characters in!" way of developing new Sonic games. I didn't care for him from day one, I don't care for him now.
The bonus stages were a step BACK in gameplay (hurr let's go psuedo3d!), and the access of them was poorly thought out (giant rings as opposed to marker halos).
Stages for Sonic 3 were pretty terrible all around (Carnival Night Zone? Do I really need to explain why this one is so bad?), and had none of the pizazz of the previous two Sonic games.
Plus, I just don't like it. Period. That should be enough.