It's worth noting that Sonic Heroes sales were up there with the best of the 2D games.
It's also worth noting that it was multiplatform (which gives in an edge over the Adventures and the originals), that gaming was much more mainstream when it came out, and that its development costs will have been much much higher than the Genesis titles.
On topic, what do I think that Sonic Team has to do to make a successful game?
1) Stop trying to be a AAA title. You're not GTA4, live with it.
2) Stop with the godawful stories and voice acting. If you must have them, decide what they're going to be and build the game around them rather than try and bludgeon them in (SRA as opposed to SSR). Have a small writing team and stop doing it by committee.
3) No more new characters. You have enough.
4) No Big. Ever.
5) No furries getting off with humans. Nobody other than PPA wants to see that.
6) Keep it simple. Don't put in a million different moves and controls, we want to run, jump and smash shit. Build a couple of gimmicks into each level to make them distinctive, and work them in in such a way that they don't just feel slapped on, they're actually a part of the flow.
7) MOST IMPORTANT: focus on making a game that's fun to play. It can look like ass, have no sound or story and have Sonic mutilating kittens on the box art, and we'll love you for it as long as the core gameplay is there.
If they do all that, I really don't care if it's 2D or 3D or whatever, I'll enjoy it.