I started with the Gamecube version, and I love the Gamecube controller.
At the moment I have the Wii version because it's cheaper, they still sell it, and it gives me a reason besides Skyward Sword to keep my Wii.
I honestly like the Wii version better because it's 16:9, you can equip 4 items at once, and I love the gold wii remote.
The gamecube is my favorite system of all time but people need to move on, so that's a personal reason I choose the Wii version.
I think that both versions are great, the Wii version might be better now a days because it's cheaper and it's not rare (which is why I have it). I had both at launch, sold them later, and now that i'm back into Zelda I got the Nintendo Selects version