If you go to SEGA’s Sonic Generation product page, you will notice that they put up a new cover. This one looks less like a place holder and more like an official retail one. If you look closer, you will see that it has the 3D enabled badge right on it.
That’s right, you will be able to play as both modern and classic Sonic in 3D. So all 3 versions of the game (announced so far) will support 3D!