My answer to this kind of sucks. It's annoying, because I know that the 2D Sonic games are almost always better. They just are. Some of the more modern ones suck because the introduce the 3D's cancerous boost and homing attacks, but I think the 2D games perfected themselves with the Sonic Advance series.
That being said, I know that 3D Sonic has the makings to be so much better than the 2D ones. There has never been a good 3D Sonic game. There have been slight slashes of potential, but even the best one (Sonic Lost World) had deep flaws. The Sonic Adventure series is literally unplayable to me. I don't understand how anyone can enjoy those crap games.
3D Sonic can be better than 2D Sonic, but the need to fix some things. And they need to take a page out of Super Mario 64 and Super Mario Galaxy to do it.
1. STOP changing Sonic's core mechanics! In Sonic you run, jump, and gain momentum. That's it. Stop it with the homing, and the boosting.
2. STOP fucking up the camera! It's 2014. How is Sonic Lost world the only 3D Sonic with a competent camera!?
3. STOP putting 2D levels or sections in the game! This shouldn't even have to be a point. This is a 3D game! Leave the 2D levels for 2D Sonic games.
4. STOP making the games so short! It's a level based game. We get it. We love it. How does Mario Galaxy have over 100 levels and Lost World can barely reach anything close to that many 3D levels?
5. STOP trying to make Sonic and action adventure game! Sonic is a speedy platformer. The game is about running and jumping, not stopping and fighting. Not exploration and puzzle solving. Enemies are made to be obstacles, not sparring partners. I can forgive Sonic Boom, because it's a spin off, but stop making the main games center around that shit. And before I get a shit storm, I'm not saying that a Sonic game can't have elements of exploration, but the game shouldn't center around it.
6. STOP dividing gameplay sections with specific characters! There should NEVER be a "Knuckles level" or a "Tail level." You get 100+ stages, where you unlock characters along the way that play pretty much the same with unique quirks for variety, and every character can complete every stage.
7. STOP adding 100+ playable characters! Sonic, Tails, Knuckles, and Amy. That's all we'll ever need.
Basically, make Sonic Adventures 2 3D with 100+ stages.