After reading this thread a few days ago, I went ahead and picked up the GC version since I never beat the game on Wii and have already traded it in. Below are my impressions.
GC Version:
Pros:
-Better combat control (not only is pressing a button easier, but there are combos you learn later on that are much easier to pull off on GC)
-Button mapping (having buttons mapped to the "Y" & "Z" button are much more accessable to me that the d-pad on the Wiimote.)
-Camera control
-Graphics (Although the Wii version looks better, it's very slight. The only difference I can see is the bloom lighting. Had they simply added more AA to the Wii version my opinion would have changed, but the fact of the matter is that Nintendo pushed the GC just about as far as it could go. The same can't be said for Wii)
Cons
-No Widescreen (why this was excluded on GC is mind boggling, but it's the main reason to consider the Wii version imo)
-Menu interface (I don't like not being able to access the map through the start menu. This option should have been added instead of having to press > twice on the d-pad)
Wii Version
Pros
-Widescreen support (this makes a huge difference, especially for people who own an HDTV)
-Aiming (this is by far better on Wii. There really is no comparison here)
-Menu interface (IIRC press the +, -, 1 or 2 button to get direct access to the menus. Navigating the menu is nice with the Wiimote, but not necessarily better. The main thing better is the way the menu itself is set up)
Cons
-Combat (the Wiimote doesn't always register moves. Combos are almost impossible to pull off and there is a delay between swinging the Wiimote and the action being implemented on screen. This made the game a chore imo)
-Graphics (although widescreen and bloom lighting is present and look better than on GC, I noticed dithering and jagged edges quite a bit more in the Wii version. There really is no excuse for this when the Wii could have easily fixed these problems)
Conclusion
The Gamecube version is the better version overall. If you don't own a widescreen TV there is no contest that the GC version is better. If you do, the GC version is still better, but not without some sacrifices. The biggest problem I had with the Wii version were controls. Had Nintendo stuck with pressing the "A" or "B" button for combat like they originally stated when the game was announced for Wii, then it would have been the superior version. As it stands though, swinging the Wiimote just wasn't fun for me especially when moves were harder to pull off. It eventually became a chore and I dreaded combat the further I got into the game. The result was that I quit playing the Wii version and traded the game in.
Coupled with the fact that the there are hardly any graphical improvements in the Wii version only add insult to injury. The fact that widescreen support was excluded from GC and that the jagged edges and dithering are more pronounced in the Wii version is inexcusable.
Look at it like this, would you rather have the swan song on GC that pretty much perfected everything that had been done before it, or play a launch game that was good, but had experimental controls? No matter which way you cut it, the Wii version is a port of a GC game. It could have been and should have been the superior version, but it's not. If you're on the fence about which version to get, get it on GC. Wait until they fix the issues on Wii for the next Zelda game.