Here's my list:
1) More characters (namely vector :P)
2) more secrets. not just secret stages, but also secret characters, secret areas, (I don't just mean rooms full of powerups, but a whole new area. I remember a shooting game, where if you shoot a certain object in a level, you would be teleported to different places, like a pool party, a duck shoot minigame, a chicken fry, a bowling alley, a billiards room, ect.)
and secret routes through the level.
3)More bonus stages. I know you only need seven, so why not make secret bonus stages? like say, find a hidden super emerald, and you'll be transported to the stage. you don't have to win anything for clearing them, but it'd be a nice touch.
4) Add Yellow Gallaxy as a standard multiplayer level. At least, if not for the level itself, for the fact that it is an homage to the most anticippated sonic game of all time. Besides, its good, and you know it.
5) It'd be nice if there were cutscenes between zones, so that the game actually has a real story. Or at least an ending.
6) A secret ending.
I am aware of the lack of space, but still...