Maybe it'll be like the rumble pack with Ocarina, where if you have it you'll feel a rumble as a clue - an extra feature that's there if you have the Wiimote, but doesn't directly affect the story. But with the amount of extra dev time involved with this one, there has to be extra content (e.g. more puzzles) in the Wii version.
This is a unique situation. Nintendo needed a reason to make people buy Wii, and since the GameCube is dying, it made perfect sense to move what would have been the biggest Cube game ever over to Wii. And if you're going to move it over to the Wii, you might as well take the time to add extra stuff that's Wii-exclusive, including the control scheme. It's a showpiece game, so Nintendo has to make it a showpiece for everything Wii has to offer, especially the control scheme. I can see why they dropped GC controls...why have them in there? Why not force people to use Wii the way it's supposed to be used, to get the whole experience? Don't let them cop out by using GC controls, that accomplishes nothing for Nintendo's mission.
This is just like Wind Waker. Before that released, people were up in arms and acting like it was going to outright suck. When everything was said and done, it turned out to be a GREAT game.
And yeah, I played Zelda at E3, and thought that the controls were fine. Aiming with the bow and arrow was too difficult, but nothing that couldn't be solved with a few more months of polish.