Hopefully the majority of games won't make essential use of the controller screen. Because doing so would preclude the other touted feature of the controller; the ability to transfer the entire game to the screen if the TV is in use.
I would guess games would have several different configurations that you could switch to on the fly. Something like tv + controller, controller only, etc...
The problem there is it would mean less straight ports from other consoles, and devs might have to have a dedicated Wii U team. And if games don't sell as well on the Wii U, guess which version gets dropped first?