Hydrocity has always been a top 3 Sonic zone for me. As much flak as S3 gets, I loved that game so much. I liked it far better than 1 and 2, even without the lockon. I think S3 takes longer than 2 as well, it has less zones but the levels are far bigger.
The music was crazy and nearly every Sonic 3 zone is excellent. Marble was probably the worst but its still better than the latter half of S2, and carnival had the barrel, but the rest is top notch. Angel Island, Icecap and Hydro are among the very best.
Sonic 3, the complete edition, is probably the best Sonic still. Its the most cohesive in level design. Mania eventually drops the ball when it comes to stage transitions. As for Knuckles campaign, in Mania there are a few levels tailored to him but its largely identical otherwise. In S3 the entire game was altered for his sake. He had much more different bosses (and basically no Eggman, as his campaign took place at a later time), his final boss was completely unique. But really, its like expecting Nintendo fans to create a game that beats Mario World.
I think this game beats Sonic 1 and 2 and thats quite an achievement for something thats pretty much a fan project.
I actually disagree, i really don't like Sonic 3 that much. I found Marble Zone quite annoying to play, same since Ice Cap which have the same repetitive pattern (those plateforme who elevate themselves with momentum) again and again. (I think one act of Ice Cap is actually better, don't remember which one) They are also strangely linear too compared to Sonic 2. But the worst have to be Carnaval Night that i really hate and find boring. It's a good thing Angel Island, Hydrocity and Launch Base are so incredibly great and the OST is so good but i always felt like the Level Design was quite inconsistent.
Finally the final of Sonic 3 is really anticlimatic, you don't even go to the super base of Robotnik, you just fight a strange machine like always which is as if it was a simple boss. (Well, the music really scream "LAST BOSS" so you take its word for it but still..) Also, maybe Knuckles have more distinct thing in Sonic 3 & Knuckles but i always found him to be very annoying to control. He tends to lose all momentum after a fly which makes him not as fun as Sonic... It's something that i found corrected in Sonic Mania which mean i could enjoy playing with Knuckles a lot during my third run.
Now, Sonic & Knuckles is really different, Mushroom Hill is a very original and incredible first world, Flying Battery is incredibly fun, i thought Sandopolis was a nice change of pace even if i have a friend who hate it, Lava Reef is very cool having a second act with a totally different setting (even if it's my less favorite level) and the climax with Hidden Palace => Sky Sanctuary => Death Age => Doomsday is just incredible all around.
So yeah, Sonic 3 & Knuckles is great but the Sonic 3 zones really put it down in my book. Sonic Mania is way more consistent, the only zone i don't really like is Lava Reef which i considered good in the previous entry !
The only problem i have with Sonic Mania is a lack of proper climax to be honest, and i think the lack of transition between certain levels are at fault. (I didn't even KNEW Sonic was in that floating giant Robotnik base from Sonic CD. I mean sure there is Metal Madness but still)
PS : I also don't get the hate for Sonic 2 latter half... I mean, the enemy placement is very cheap, i agree, but it's the case with the rest of the game. Hill Top is quite fun with its lever mechanics which made me think of some Lode Runner cartoon and the lava/Earth Shaking, it feels like a better designed Marble Garden Zone to me since it's actually NOT that linear. Mysitc Cave is also quite fun to go around with switch which open new ways and stuff like that. There is this "that one hole" with spikes you can't climb back and i fhink everyone fall into that one but other than that i quite like it. Oil Ocean with its fans can be a little boring indeed that being said, but i quite liked the thematic and music with it which mean it has that compared to Carnaval Night. Finally, there is only Metropolis which, indeed, didn't needed 3 act (even if each act have a different "main" mechanics). The enemy placement is especially bad in this one too so if people don't like this one, i can really understand. (Even if i found the plateforming quite good myself, as far as "somewhat linear zone" goes, i will take original metropolis over any original metal madness for example)
Finally the final with the shmup session and boarding the final base of Robotnik was really good and created an awesome climax with my favorite last boss of the serie... Really, can't go wrong with that one (even if the shmup session is a little annoying when you replay the game now... But that's just one act and it's shorter than previous levels).
No really, i can't say every levels were good in the late half of Sonic 2 and the bad enemy placement clearly annoys me but it wasn't clearly as bad as, say, Level Design of Sonic CD or Marble Garden Zone.