The folks over at Cubed3 have put together a very impressive mock-up video of how the upcoming re-release of Wind Waker could play once it's prettied up and released on the Wii U. Keep in mind that absolutely non of this is official and the graphics are just the GameCube version.
They go over a wide variety of control schemes, from using just the GamePad and its buttons, to stylus movement a la Phantom Hourglass, and even include Wiimote + Nunchuck controls. There's some great ideas in here, especially using the GamePad as the Tingle Tuner. Definitely check out their ideas, along with explanations, on their website.
I trust Nintendo to do a solid job with this re-release, and I hope that some of these ideas are integrated into Wind Waker Reborn, releasing later this year.
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destructoid's previous coverage: The Legend of Zelda: Wind Waker Reborn