I've only played the Wii version, but im gonna say Gamecube lol.
It is the Canon version, and i don't like the flipped map (though it's what im used to)
Also the controls. Skyward sword was what the first zelda wii title should've done but TP didn't do that. They had the little waggle and some nunchuck thrusts, plus some aiming for shooting things. Don't get me wrong, I love these, but if they didn't have any substantial use foir the wiimote, just use regular button controls so i dont have to hold my wrist steady everytime im aiming at a hookshot target at an awkward angle
I have only played the version of the Wii, but from the looks of the Gamecube controller with the c-stick....I would say the Gamecube one would be better. I am the person that likes to have freedom on camera angles on games.
GameCube version had far better controls IMO. They hadn't gotten it down quite right and it felt really gimmicky to me, whereas the GC version felt tight and controlled. SS eventually came along and fixed the motion control issue, but I still like the GC version better.
I really can't have a vote on this so i didn't pick one. I think you should have both of them, maybe i'm just saying this because i'm a collecter... but I think you should have both so you could experience them.