Wii U tablet controller can act as some form of link to the Assassin's Creed "Animus"
Wii U tablet Animus can be used as a persistent on-screen map and navigation tool.
Animus Database entries that may pop up from time to time, could be displayed on the touchscreen instead and not interrupt the flow of the game.
The Animus can also act as an encyclopedia of information. Character biographies and bits of information that would normally be cast aside could be displayed on the touchscreen (take a break and read up on the side story & character history while eating dinner?).
Easy touchscreen weapon selection during combat. Quick change from dual-wield combat to single with a simple touch.
Using the touchscreen as an alternate view for Eagle Vision. Using the built-in accelerometer to control the camera view while in Eagle Vision.