This is definitely going to be a weakness for the Wii U for Devs in the long run. Devs feel obligated to use the gamepad just because its part of the system. Dice, Gearbox, and Crystal Dynamics all appear to be on this boat.
It has always been a weaknes for Nintendo every generation. The only strong 3rd party after all these years were Japanese third parties, until Sony snatched them with Playstation.
I say that Nintendo will regain back Japanese third parties, but western third parties will continue to shun Nintendo