Ok, well, people here don't seem too high on Wii U, but I can't help to think of the possibilities. Now I know we did this with the Wii and were disappointed, but why don't we take a second and just think "what if?".
My first thought when they showed Batman is using the screen for Detective mode. One of the main complaints about the first game was that there was no reason not to use Detective mode the whole time. If you make it so that you have to hold the controller up and what you see on the screen is relative to where its positioned in relation to the TV, detective mode could be used on the controller screen only.
I also like the idea of using it to mark places on a map for an open world game. Having the map on the controller would make traveling a ton easier.
Any other ideas?