Here're a few that I'm hoping surface eventually:
-Smash Bros.
-Viewtiful Joe (Since the games take place in "Movieland", and the movie industry pioneered 3D, Joe could gain new 3D VFX powers.)
-A new Pikmin game -since we've heard nothing about Pikmin 3 >.< -
It's my job to help the next generation, and set a good example for them. And for that I'll gladly lay down my life.
Both a Galaxy game and a Brawl game could be successful in combination with 3DS-unique features like the obvious 3D technology, the larger upper screen, and raw processing power. Wishful thinking, but they're fun ideas.
I second this with the power of impure thread resurrection. AW is not known for flashiness but some 3-D flare tacked onto map elements, map animations, and battle animations could look very cool. The 3DS probably has a good enough GPU to warrant animated cutscenes sprinkled in there too.