Same problem like in the current
OoT remake thread. New play control based on what? Twilight Princess? Nah, even Nintendo theirselves said, that Twilight Princess for Wii wasn't perfect at all in terms of controls. And we don't know, how different the gameplay and controls will be in the upcoming Zelda Wii. Both maybe won't fit for The Wind Waker.
But so far except for some fun stuff like Jungle Beat Nintendo prefered to have their NPC titles based on later installments of the corresponding series. For example the Metroid Primes are based on Corruption's controls and both Pikmins are probably based on Pikmin 3's controls. They can't let The Wind Waker be based on Twilight Princess, we don't know anything about the next Zelda on the Wii and The Wind Waker isn't exactly material for coming up with some cheesy new "bongo bongo waggle waggle"-controls.
So, no, The Wind Waker probably won't be part of the New Play Control! series. There are other GameCube titles, that are suited better for that, Luigi's Mansion or Mario Kart Double Dash (with online play) for example would be nice NPC choices.