So think about it a 3D sonic game that's sandbox style where you can just do whatever you want: go on an emerald hunt, fight eggman, fly in the tornado, use super transformation, anything! How do you guys think that would work out? And please just give it a chance and think about it before you criticize it.
Actually it could work, Certain things could open up for later use, for example: The Tornado might need to be used for a fight in the sky; and then you can use it whenever you please after words ( or just for more "Tornado Sidequests).
Emerald hunts; could be slightly different, the only way I could think it would work would be using the "Emerald radar" and finding it before eggman does, if he finds it, you have to attack him before he escapes,and if he does end up escaping you'll have to steal it back from his base.
Fighting Eggman is just simple; make it a plot quest...Maybe he can be in a giant mech, or send a robot after you ( Metal Sonic fight anyone?)
Super form is slightly tougher...The way this works could be if you have all 7 chaos emeralds before a final fight ( this could mean you can get the emeralds before eggman even knows of them via Special Stages or buying them off someone ( Nack, Rouge, etc.)). after that you could buy the skill "Super Transform" and have access to it.
And I think it would be cool to have a similar concept of being good or evil, similiar to inFamous; where Sonic could chose his path as well as perhaps have more Abilities to have access to...
Sonic is a platform game character, and I don't think that that could be translated too well into a sandbox-style game.
It could be translated, not well, but translated...an example could be the generic "Run through rings" missions, they would work; but it would be obviously something everyone has done... So the challenge is finding something Sonic could do for a side quest that isn't Generic, but also fun...
tl;dr: It's possible, but it just wouldn't work, what needs to be done is find some quests that would fit Sonic's abilities while making it entertaining for the player...