Remember how with Sonic&Knuckles you could plug other games into it to get S3&K (with saves), or S2&K? (I've also seen a hack to allow S1&K)
Sonic 1+2+3&K, all the levels chained together, with the save/load from S3, and an expanded character select. Sonic, Tails, Knuckles, Amy (mostly as a Sonic resprite), Cream (mostly as a Tails resprite), and MAYBE Shadow or a couple other characters from Chaotix or the Sonic arcade games. 1-player with any, 2-player any 2 (Not limited to certain combos like S&K, which only allowed Sonic+Tails or Knuckles+Tails in 2-player) And of course give Tails/Cream Tails' flight ability from S3.
And of course update the graphics to HD quality, and to widescreen display (by displaying more of the background/etc, NOT by cropping out the top and/or bottom of the background, and /certainly/ not by stretching the picture!) I'd also suggest keeping the miniboss music from S3 instead of replacing it like S3&K did, but that
(Maybe even throw in some of the Sonic 2 Beta levels taken out of the final, and use the music/graphics from S2B for the S2 levels instead of the S2 Final music/graphics? That'd be nice.)