It's rather evident the Wii U GamePad makes for a plethora of options in terms of gameplay; its touchscreen, dual analogs, and two additional trigger buttons are begging to be explored for use in Zelda Wii U. And while the Classic Controller Pro for the Wii did have the dual analogs and extra triggers, they weren't implemented in Skyward Sword because of its Wii MotionPlus controls, but I think now is a great opportunity to do so.
First and foremost, the touchscreen should definitely be put to use, but I'd prefer it to be optional. One thing I'm really hoping for in Zelda Wii U is for the Wii U Pro Controller to be available for full use within the game. So what then can the touchscreen be used for? Well, as shown in the E3 tech demo and the upcoming release of Batman Arkham City: Armored Addition, the touchscreen appears to be perfect for instant access to menus; it could be used for anything from quickly changing Link's current item (similar to Skyward Sword's functionality of the B button) to pulling up a map without taking away from the on-screen action. Of course, the problem is evident that you would have to take your eyes away from the main screen and essentially have to pause anyways, which is why I think this should be optional as stated before. It would add an extra level of difficulty to the experience, which could subjectively be viewed as either a good or bad thing. Thus, with the technology available, it's only logical to have it optional.
Another thing the Wii U GamePad touchscreen could be used for is puzzle-solving. It could be used to get an overhead view of a block puzzle, for example, and the player could optionally move the blocks on the touchscreen while using this overhead view. Of course that's only one option of many, but I think using the touchscreen for puzzles is a mixed bag; it could be beneficial, but if so, not prodigiously.
And then there are the dual analog sticks. One thing I'd love to see return to the Zelda franchise was an excellent feature from The Wind Waker: the free camera. The player could do a full 360 of Link's environment, which allowed for more in-depth gameplay and to peruse his surroundings to solve puzzles or just observe the incredible scenery, which in turn fabricated a great experience. Of course, this was also available in Skyward Sword, but it was a button away and forced the player to go into a first-person view. I'd rather be able to simply move the second analog stick and keep the regular third-person view, which was available only in The Wind Waker.