Sonic the Hedgehog - Marble Zone (Along side Green Hill Zone). 
Sonic the Hedgehog 3 -  Ice Cap (were the fuck was Sonic 3 anyways?).
Sonic Adventure - Windy Valley.
Sonic Heroes - Hang Castle or Mystic Mansion.

None of Sonic Heroes. Oh, wait. Also I think Sonic 3 just got bunched in with Sonic 3 + Knuckles, maybe a little unfairly considering there is a Sonic Heroes stage.

Sonic 1 - Spring Yard Zone

Sonic 2 - Mystic Cave

Sonic CD - Wacky Workbench

Sonic Adventure 2 - Pumpkin Hill

Legit Anything From Shadow the Hedgehog

Sonic 2k6 - Radical Train

Sonic Colors - Sweet Mountain

Is Flying Battery in it? Loved that music.

Ice Cap Zone is a pretty big omission.

Marble Garden from Sonic 3. Think of how it would look in this game.

@Allison I agree with Pumpkin Hill! I loved the song to it xD.

There are a ton of really cool stages that have been used and made through the Sonic Timeline.

I think some of the ones from the Sonic Advance series would have been really cool just to see them rendered in 3D and they were made to be really fast.

I had like a list of specific stages then I click the link and they like all leave me D: