Both were masterpieces, but I happily bought my GC version over the Wii version for the following reasons (oh, and yes I have thoughourly played both:
1. The wii version was nothing but a port - I agree the controls were tacked on. Besides, sword fighting didn't feel immersive if you had less control over exact combos by waggling the wiimote over precise button + joystick. There was also a learning curve, but I admit fishing, bow + arrow and the spin attack felt great, if not better than the GC version.
2. The wiimote speaker - I absolutely cringed when I heard the Zelda chime. It was god-awful. It felt like a grind rather than a chime. And while the midna laugh was charming, it was a tad annoying at times. But worse of all, when Link was slashing and hitting enemies, it sounded like I was flogging someone with something made out of rubber or plastic. The GC sounds were much sharper, crisper and better. Dolby Pro Logic II > 6 KB of walky-talky quality sound
3. The lack of extra features and implementation - the Wii version has 3x the RAM, umpteenth amount of disk space and approx double the power - so why are there NO extra features or enhancements whats-so-ever? Not even an exclusive minigame? And if you were to incorporate the wiimote, why did you limit it to few items? Why couldn't I control the ball + chain with the wiimote?
The first true Zelda title will come in 2009 when there will be a ground-up Zelda title with deeper controls and a different setting.
Optusnet
1. yeah it was a port...but other than that, you complimented the game. 2. yeah, the wiimote sounds terrible, but you know you can turn it off right? thats what i did. 3. again, it was a port. had they NOT made this for the wii, and just released it on the GC, people would be complaining, MEH MEH MEH, why can't i play this with cool wii controls?! 
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