Just like Windwaker HD. Non-intrusive, interchangeable with a Pro Controller but using it had some nice perks (inventory omg so nice), and could be used to go to the Miiverse.
WW HD is my favorite game, and I only ever played it with the Gamepad, because it felt really natural.
I would not mind there being Minigames, like solving a Jiggy Puzzle equivalent, using the Gamepad. As long as it's something that could also be done without the Gamepad for pro controller users, I think it'd be neat.