Ahh, Scrap Brain. That would be cool...Sonic could have these most likely:
Sonic 1
Green Hill (I think this has a high possibility, who doesn't think this zone should be it?)
Scrap Brain has some possibility... (They could have those floors that open up and cause you to fall off the stage...)
Dude, the only one from Sonic 3 there is Angel Island, the rest are Sonic & Knuckles...Sonic 3
Angel Island *see other post*
Sandopolis has many possibilities as well...
Hidden Palace
Sky Sanctuary
I figured if there was a stage from this game, the best contender is the floating island, with the shrine on it, and Chaos as a Stage Hazard, Egg Carrier & Station Square a possible second.Sonic Adventure
Mystic Ruins where you fight Chaos and Knuckles... that area might work...
Egg Carrier (but it'd probably be very much like Halberd..)
That area where you fight Eggman last as Sonic (egg viper)
Sonic Adventure 2
Green Forest where Sonic and Shadow fight
Pyramid Cave Where Sonic/Eggman fight Egg Golem
Meteor Heard Knuckles and Rouge fought there...
I just picked what I felt would be creative... I might get my art skills and make some mock ups of what stages could look like for those levels, the possibilities are quite honestly endless.
Pyramid Cave would be cool, and it could have multiple levels to it... On the first level with the Egg Golem attacking you, until it got sick of you and just wrecked the platform entirely, sending you down below onto moving blocks in the sand, with those monkeys throwing bombs at you in the background...