How about a good 2D Metroid game. There hasn't been one since Super Metroid (Oh yeah...I said it).
A new Chrono game would be super awesome. Please not on a handheld though.
A true sequel to Super Mario RPG. The spiritual successors have never had the same feel.
How about Nintendo gets to making Eternal Darkness 2. Silicon Knights exploded but there must have been enough there to get the game going. Just leave Dyack out of it plz.