Based on some of the remakes and remasters already on the Wii U and 3DS (Wind Waker, Star Fox 64, DKCR, etc), I'd say that the 3DS is best suited for a DS or N64 game and the Wii U is better for a GameCube or Wii remaster. Older games can simply be on the Virtual Console while on the 3DS, even GameCube levels can be tricky at points.
For the Wii U, I'd pick F-Zero GX. Part of this is because Nintendo has not made much like this since the GameCube, but I also feel this one game would greatly benefit from an update. You have thirty racers at a time zooming along at high speeds, something that would benefit more from the 1080p 60 FPS treatment than, say, Paper Mario. Online multiplayer, even if simpler than in MK8, could make this game more alive than ever before. Plus, this game is not very common in the wild and is not possible to play like Wii games are.
For the 3DS, I would like Super Mario 64 with the DS version's content. I normally wouldn't want another remake of the same game one gen later, but the DS version was really a mixed bag. I loved how the 3DS version added so much content. I feel the three new playable characters was somewhat unnecessary, but the extra star for each world, extra few stars in specific stages, rabbits to catch, extra minigames, and visual updates are appreciated. If a version that combined actual analog control with the extra content existed, that'd be great.
