I think the level design can be pretty confusing at times in this game. The stones that were swinging back and forth looked more like platforms that you could roll around atop of, so I kept wondering what was wrong when I was trying to get on top of one while I was invincible. You can figure out what happened after I lost invincibility.
I do like that you made seperate paths for Sonic, Tails, and Knuckles, but it wasn't always easy to figure out where they were supposed to go. When I first got to the part in act 3 with the moving platform and tons of spikes, I assumed that it was Tails-only because I didn't see any way for Sonic to get over the spikes at the time, so I went back and got lost. When I returned, only then did I see the platform inch into the screen. Knuckles had a completely different path on the bottom half of the level iirc, way off course from where Sonic and Tails were supposed to go. I would suggest moving pathways that split right next to each other like the end of Angel Island act 1 in Sonic 3.
Presentation is nothing I've ever seen in a fangame though. Congrats on the amount of effects this game has and story elements as well. It's kind of inspiring, infact.