Personally, I enjoy the Wii version more. I own both versions, but I've never played on the GC one after I finished it.
The thing about it is that even though I play the Wii version, I switched all of the controls over to the classic controls. XD So, in a way, it's a mix between Wii/GC Twilight Princess. Your sword is still swung by shaking the Wiimote, but you don't aim by using the pointer -- instead, you just aim the classic Zelda way by using the Control Stick. I turned off the pointer as well.
I like the classic controls, but something about Wii TP does it for me. Contrary to what other people have said, swinging your sword isn't that much of a big deal. It never tires out your hand. If it does, then you're overdoing it. I went through the Cave of Ordeals twice in a row and didn't get tired one bit. :|
There's only two main problems I have with the Wii version, and they're the fact that the Shield Attack is hard to execute sometimes, and that there is no free camera control (with the C-stick). I love the Helm Splitter, which is a Hidden Skill you learn, and the only way to do it is by doing a Shield Attack and pressing A afterward. The problem is that if you shake the Nunchuk, you do a Spin Attack. Sometimes I'm trying to do a Shield Attack by thrusting the Nunchuk forward and it ends up doing a Spin Attack. -_-;
And yeah, there's no free camera control. You can only switch views the way you could in Ocarina of Time/Majora's Mask by Z-targeting.
But on the bright side, the Wii version has widescreen capabilities and slightly better graphics (although this really doesn't matter much). The powerful Spin Attack is much easier to execute. The controls are arguably smoother than its GC counterpart; this is all personal preference. While I may feel like it's more natural than pressing B, a great deal of people prefer the classic way over shaking the Wiimote.
On the other hand, the GC version has everything a classic Zelda has. It's a pretty balanced game and there's really nothing wrong with it other than the fact that the Spin Attack takes a while to charge up if you don't know how to do the quick 360 on the Control Stick and press B. :\
I prefer the Wii version, but I suggest you to get the GC version.
