I think Nintendo should create a RTS game with all nintendo races. Races like Mushroom Kingdom, Hyrule, Pikmin, Donkey Kong Country, etc. It would be something like Starcraft in a way. They could also make Hero characters that are stronger then normal units, like Mario, Link, etc. These hero's also should be able to level up in battle and unlock new abilities.
The game should also be multiplayer, not only online but local. one person could use the game pad and the other could use the tv and wii remote.