It's obviously going to use the game pad.
Watch them implement a camera and a bow system with it. There's already a bow section in Nintendo Land that works great, it's also been implemented in WW HD, so with the focus on the bow in the only preview we've seen, I wouldn't be surprised if targeting weak points with the game pad isn't a thing.
If nothing else, it makes inventory management and map browsing so much more convenient that it'd be a crime not to use the game pad.