Stealth Inc. 2 is a a great example of a how the GamePad can/should be used in some games.
Here: https://www.youtube.com/watch?v=nq7u8zaFZGM (watch the whole video)
I think that developers aren't creative enough or don't even give it (Wii U) a shot. The GamePad opens endless possibilities; Minecraft on it would be THE DEFINITIVE WAY to play.