My big beef with the 3D Sonic games (other than what I said about the "OMG SERIOUS BUSINESS!") is that, well, you rarely get to actually play as Sonic. This wouldn't matter if the other characters' levels were, you know, fun. If I wanted to play a bland shooter or a poorly made treasure hunting game, I wouldn't be playing SONIC. Sonic games need to be about running fast, and crazy platforming--while running fast.
My other problem with the 3D Sonics is that they all have the same problems... Sonic Adventure 2 and Heroes (I won't open up the old wounds of Shadow the Hedgehog) have the SAME camera problems as SA1. The camera isn't incredibly bad, but it's bad enough to detract form the fun. Sonic deserves better than these half-assed sequels, and thankfully, he still gets the quality he deserves in his 2D games. That's not to say these games don't have their shining moments of awesome... they're there, they're just far too few to make up for the other gameplay flaws.
3D Sonic could (and should) rule, but Sonic Team, for whatever reason, doesn't want to put in the effort to fix the problems with the Sonic Adventure formula.