I really don't see anything in the game that needs fixed. It to me was a perfect game.
Updated graphics would be awesome, but I would like for it to be true to the original, and to be honest I would be completely satisfied with a 3ds port.
Ooooh, I thought of a good one. Mario. Paint. I would buy the heck out of some Mario Paint U. I mean, the console has a freaking drawing tablet for heaven sake! Why wasn't there a remade Mario Paint with shiny new graphics and more features made for the consoles release? Imagine Mario Paint U coupled with Miiverse- people being able to post animations, artwork, and music they'd made? I think that'd be awesome!
Umm...Warioware DIY used some things from Mario Paint and added some more different features but sure, why not have a sequel. I mean. I can't really connect to the internet on DIY like I'd like to so that would be just fine.
The 3DS should remake Super Mario 64. I know it was done on the original DS, but the 3DS could easily fix a lot of issues the original remake failed to do such as:
1. Co-op at last, now that limitations are gone (maybe online co-op).
2. More hidden levels.
3. Rideable Yoshi (if they decide to just have Mario in the remake's remake).
4. Optional to do two quests: one as just Mario or as the characters introduced in the first remake.
5. More levels/hidden castle areas.
6. Framerate at least higher than 30fps to insure a fast experience; maybe 60fps.
And an option, for just the Mario quest, to play the classic Super Mario 64 after you complete the Mario quest of the game. Like how Metroid: Zero Mission let you play classic Metroid upon completion of the game.