Nintendo is ubiquitous with platformers (there’s no getting around it) and they have most of the other genres covered, such as the RTS (Pikmen) and RPG (Mario & Luigi series). But there are a few genres which are under represented by Nintendo such as an old school point and click adventure or a top-down hack and slash in the vein of Diablo in which item management could be made a lot simpler on the Gamepad.
As I have said before a new IP carries a lot of risk, but a way to circumvent this is to reinvent an existing franchise into another genre. Metroid Prime was a huge success going from a side scrolling action/adventure into a first person action/adventure while still retaining the core elements in the series.
The most suggested idea I have seen is an Pokémon MMORPG which makes perfect sense and would remove the hassle of having to transfer Pokémon from one game to another. The reason I can’t see Nintendo doing this is because Pokémon has become a foundation for their handheld platform and helps shift units while also keeping their handheld systems relevant. Many people only buy the portable consoles to play Pokémon.
So which genre would you like to see Nintendo attempt next?