I had trouble finding concrete, neutral impressions on which of the two versions is best. Most "reviews" just assume the Wii version is the best. Most reviews barely compare the two since the reviewer had already been playing the Wii version for months before the cube version hit stores.
I have recently spent some time between the two versions. I have primarily played the Wii version. Here are my impressions. I will speak of it in terms of the Wii version compared to the Gamecube version, instead of giving pros and cons of each.
The first thing I noticed was that the image quality seemed worse than the Gamecube version. This is likely due to the anamorphic widescreen. What this means is that the same 480 lines of resolution are changed into non-square pixels and spread across a greater area. Many games suffer some loss in image quality due to this (a great example is Super Paper Mario). I do admit that the widescreen is nice. It should be mentioned that the meat of the gameplay and menus are still constrained to a 4:3 area, so the extra viewable area on the sides is just icing on the cake.
The flipped world didn't bother me at all. It was insanely confusing when I first switched to the Gamecube version, but I got used to it. I haven't played Ocarnia of Time since it was first released on the N64, so I can't comment on how annoyed a long-time fan of that game would be with the flipped world.
What about the waggle? To be honest, after playing Wii Sports Resort, all waggle feels pointless, but this game takes it to the extreme. Every attack is just waggling the control while hitting different buttons. Want to slash? Waggle. Jump and slash? Waggle while holding A. Spin attack? Waggle the nunchuck. The controls do not feel intuitive at all. I found myself constantly using Z-targeting, which is exactly how you resolve combat on the Gamecube. So the Wii controls were actually a hinderance for me in normal combat. I have to admit that ranged attacks felt much more natural, however again, I found myself using Z-targeting anyway, so the benefits were small.
I think the ideal controller setup for this game would be the same as Super Mario Galaxy. SMG has waggle, but it is only for the spin attack. This would have worked great here. Use the normal buttons for combat and waggle for spin attack.
I am all for games using motion controls and the nunchuck combo. I am the guy with 100% wheel use in Mario Kart. I am the guy who strictly uses the motion controls in Punch Out. The motion controls in Twilight Princess, other than the ranged targeting, are pointless. I am greatly anticipating the next Zelda game for the Wii, which will hopefully have Wii Motion Plus support, but even without it, I assume the motion controls will be much more developed than they are here.
One last thing that many people would never notice. The load times in the Gamecube version are slightly shorter. When traveling to a new area or going in a building, the already short wait time is about 1/3 less on the cube.
My decision: Gamecube. The two major Wii bullet points, widescreen and motion controls, ended up being a minor addition and an inconvenience, respectively.
I am interested in others' opinions and experiences.