I only have the GC version but I played TPWii at my uncle's house and honestly have to say it is superior. Like Destiny, I don't agree with motion controls. But, I look at a 16:9 Hyrule Field and I'm blown away with the presentation. I wish the GC version could do that, but alas it won't be...
I've never played the Wii version as Human Link (only trekked through Lake Hylia as Wolfie at my uncle's house), but I think you ought to get the Wii version. It has a bit more to offer in the way of minority (faster load times, 16:9 display, better gameplay supposedly), but has less glitches...