Are we limiting this thread to a discussion on new controller possibilities or a more general discussion of new features to introduce in a Wii U Zelda title?
As far as the Game Pad goes, its most obvious use was already demonstrated through the Zelda HD experience from E3 2011 namely clearing the TV's HUD for a smoother console experience. After viewing the ZombiU game announced at this year's E3, however, I believe Nintendo could go a step forward by offering a new perspective or viewing lens through which to use items further adding immersion to the experience.
In regards to the title in general, I'd prefer for a variety of controls to be available from Wii Motion+ and Nunchuk combo for pure motion control enthusiasts (JuicieJ) to Game Pad for moderates who prefer to see innovation on display in a more traditional fashion to Wii U Pro Controller for those who want to play it completely traditional. Seeing as how Pikmin 3 already has two of the aforementioned control methods incorporated, this shouldn't be too immense of a task. Or perhaps the player solely uses a Wii Mote+ and Nunchuk combo or Pro Controller with the Game Pad merely offering a world map, a standalone accessory.
Moreover, I'd love to see a combination of boss battle mode and a survival like dungeon in the Wii U game. Both new elements are well incorporated and innovative and seeing them work in tandem would be glorious. We already saw this partially occur with the Lightning Round Challenge and Bokoblin Horde in SS but it's high time to raise the bar to an all new level.