I would still have to go with Sonic 3 & Knuckles, I generally tend to prefer the 2d Sonic games even if there are a few 3d games I enjoy and that game had it all. Great soundtrack as per standard colorful graphics, tight controls and lots of gameplay variety. Not to mention an unrivaled amount of content at that point considering it was originally 2 separate games. Sonic 2 was great and is probably the slightly more iconic game but it can't really compete with the amount of depth 3&Knuckles has.

I like Sonic Generations and Sonic Colors but those game did still have things I found annoying even if they're more me being nitpicky. Why did you have to acknowledge the existance of Sonic 06 Other than those two my opinion on 3d sonic games range from highly meh (adventure games, unleashed, lost world) to atrocious (boom, 06, the secret rings/black knight) aside from heroes which I haven't played. Those all somehow strayed from the path of what I think makes an enjoyable Sonic game. Often through having unnecessary gimmicks and just being plain messy in concept and execution.