I seriously hope that Wii doesn't allow people to use the GC controller for Wii games, at all. All you people complaining about how you don't want to hold a remote up forever, I have a piece of advice for you: Don't buy the Wii. There are two other consoles coming out, with normal two-handed controllers. Play one of them. The Wii will only be hampered by letting people use the GC controller, as it's then allowing any third-party publisher to port their crap titles onto the Wii. If people buy a Wii, it's because they want a whole new way to play games, and they want tons of innovative titles, not degraded ports.
I know what you're thinking too. "Hey look, it's just another Nintendo fanboy." Tell me, would a Nintendo fanboy sell his Gamecube after having it for only one year, so that he could buy an XBox? Nintendo crashed and burned with this last console of theirs, and bringing GC features to the Wii can only spell doom in the long run. I will buy a Wii eventually, I'm sure of it. Games like WarioWare, and Zelda, and even Cooking Mama, that use the controller for truly engaging gameplay, gets me more excited about gaming than I've been since I got my Super Nintendo 10 years ago.
I guess what I'm getting at here is, the Wii wasn't meant to be a hardcore system by any means. It's a simple, light, and fun system, and so using the remote to make things even simpler was one of the most genius moves Nintendo could ever make. When you're flipping through channels on the TV, you don't say "God this remote is annoying I wish I could change channels with my PS2 controller." Great things are about to happen for Nintendo, and I only hope they'll choose to go full circle and not use the GC controller except for GC games, so that in the end they'll have a machine that will truly stand alone in this "console war."