From the impressions I've read and seen, no one really seems to think the inclusion of Wii controls makes the game better to play. If you go to Nintendo's E3 coverage, they have a bunch of videos showing poeple's reactions to playing the Wii on the show floor and all the people playing Zelda on the Wii are the least excited compared to those playing other games. There's one guy who admits he doesn't care for Zelda but was surprised by how he was able to control the game pretty well but he still didn't seem that interested in the game.
This was talked about in a thread before about how if Zelda is the first game people play with the controller, the controller needs to prove that it's better than the current set-up. If it doesn't do that, it makes the controller look bad. At the same time, if it is much better, why bother buying the Gamecube version? It's inferior.
Now, all these issues aside, Zelda is no doubt going to be a great game with a great story and gameplay and graphics. And I'm sure it will do well and be hailed as a great achievement. It just seems that Nintendo is dropping the ball lately with some of their decisions about it causing all these issues to overshadow the game. To me, right now based on what I've seen and hard, I'd buy the gamecube version. At the same time, I feel like I'll be missing out on better graphics and some extra things put in (Navi's an example) and so I should buy the Wii version. But then I'm not sold on the control for the Wii version. It's a horrible cycle.