As for Super in general, as cool as he was back in the day, he certainly has been getting some nice new effects to make him stand out. Is there any chance we'd be able to incorporate these kind of things? (I know we're going retro but not everything new is bad).
Recently he's gained the gold aura and is much better at floating that he used to be.
Personally I'd like to see us really go to town on Super; for starters give him a full sprite sheet instead of a half assed attempt like the previous Sonic games (DUR DUR HEY I LOOK UP AND MAH SPIKES GO 'WAY! That always bugged me) but obviously that means deciding on a style first.
Him floating instead of standing for his idle pose would be pretty cool, perhaps grasping his hands in a "world in my palm" pose when he's waiting (or even playing with a chaos emerald?).
As for Sonic's actual transformation, how about making the emeralds appear around him for a brief moment as he transforms? You jump, jump again (or whatever command we're going for) and he pauses, the emeralds appear, circle quickly then fly into him, cue bright flash and Super is unleashed on the 2D world to wreck havoc >=3
It always seemed odd that when Sonic turned super in Sonic 3 he lost the ability to insta-shield. Sure it wasn't needed for defence any more but it felt strange not being able to do it. If Super got a larger flamey/energy insta-shield (say double the size of Sonic's, allowing him to take out multiple enemies in one blow) that could be a nice and fitting technique for him.
Are we going with a yellow or gold Super Sonic btw? I always got the impression he was meant to be golden originally but it did certainly vary depending on what images you looked at. He's gold now, but we're doing the retro thang so it'd be a good thing to decide as it'll effect any sort of shading on the Super sprite.