I won't vote in your poll because that decision is yours to make but here is something that might influence your choice:
GameCube Advantages
- Full Camera control with the C-Stick.
- Rollgoal is incredibly easier.
- Sword attacks are much more precise, even things such as Hidden Skills (Shield Bash comes to mind).
- You can hold items like the boomerang for a moment before going to first person. This comes in handy if you just want a quick move.
GameCube Disadvantages
- Only two item slots. Every 3D Zelda had three, but the Z button is reserved for Midna.
- There's some slowdown if there are too many particles on screen. Nothing hazardous.
Wii Advantages
- There are four items on the screen, but it works differently. There's one active item (
, while the rest are your on-screen reserve that you can swap on the fly.
- At least the aiming feels more natural on the Wii.
- The game is smooth the entire way though.
Wii Disadvantages
- The Wii version doesn't have complete control. It has the same control mechanic that OoT had.
- Rollgoal is nightmarish on the Wii.
- Fishing could have been more interactive, but it really doesn't matter. Reeling is the same as the B button.
- There's too much info on the right of the screen. It can obscure some things on the screen.
Miscellaneous
- There are some different glitches in each (GCN is generally less glitchy since it was released a bit later).
- There are different opening demo movies. They're mostly the same, but some things like Midna's appearance are cut differently.
- In the GCN version, holding B as you run makes Link hold his sword out as if getting ready to strike. Also, you can backflip off Epona in the GCN version, but you can't in the Wii version unless there are enemies around.
- There's a widescreen option on the Wii. I'm not putting it as an advantage or disadvantage because there's a flaw in it - you see some more of the view horizontally, but the top and bottom have been cut. It's kind of artificial due to the game's GCN programming.
- Link spins his sword differently. In the Wii version, you can do it on a whim, but you have to wait for it to recharge. In the GCN version, you have to stand still and charge it at anytime (or use the rotation method). Some prefer the Wii version, but others think it makes the game too easy.
- The game is mirrored on the Wii. That means that left and right are swapped. This is something done toward the end of development because it was noticed that most players used their right hand for the sword swings, and they didn't have time to recode a right-handed Link, so they opted to do this the easy way. This results in some errors such as the sun rising in the west, the Hylian language, and even the Triforce. This is a big change that can disorientate those used to one version of the world, but it's listed here because it's not necessarily a good or bad thing.
They both have their merits, but keep in mind that the game was built for the GameCube.