Yeah...I was one of the people who complained about the "tacked on" controls for TP on Wii. However, even though the controls are still somewhat tacked on, the controls are 100 times better on Wii than Gamecube.
I borrowed the GC version of TP from my friend just for the heck of it. It just felt weird...not because of the mirrored game world (although that was confusing after playing the Wii version), but the controls are terrible. Just wait until you get the bow and clawshot. The aiming is SO SLOW and annoying as heck.
Also, to use the spin attack, you have to do a full 360 degree rotation on the analog stick to get it to work. Whereas, with Wii, you just shake the nunchuck a little for spin attack.
So, I guess my point is that even with tacked on controls, the Wiimote + Nunchuk is still much better than a standard controller for games (not all games...fighters and racers suck on a Wiimote + Nunchuck). Seriously...anyone who owns TP Wii, go play TP GC and you'll see what I mean. The controls are that bad. I can't believe the GC version scored 0.1 higher than the Wii version.
AvIdGaMeR444
You're right about the aiming. However, there are a few points you've missed: 1) The spin attack. This is actually one of the major differences between the versions, and you have not fully explored it. The move you described (full 360 degree rotation + button press) is more difficult to execute than shaking the nunchuck on the Wii version, but it has an advantage - there is no recharge time afterwards. This means that on the GameCube version of the game you can execute spin attacks consecutively with almost no delay between the attacks, which is just awesome if you have the Great Spin technique. This is completely impossible on the Wii version. 2) Horse combat. Several moves are available in the GameCube version that are not in the Wii version - you can manually duck/crouch in the saddle, as well as execute a somersault dismount from a gallop. 3) Full camera control. This is not an incredibly huge deal as the game has a very excellent auto-camera, but it is a point in favor of the GameCube version. 4) Nunchuck and Remote aren't suitable for racing games? Mario Kart would like to say hello, because while people can't agree on the issue of analog stick versus wheel, the one thing that is clear is that either the Wii Wheel or the remote+chuck setup are superior to the GCN/Classic controller. 
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