Here is my opinion.
1. Whoever says Wii version has better graphic than GC version are very young teenagers who don't know anything. And there are so many of those people. This is why xbox360 and ps3 users are making fun of nintendo users because more than half of nintendo fans are so immatured and ignorant.
bottom line: wii version = gc version, and so many elementary school kids playing zelda.
2. wii control is innovative, but that doesn't mean it's more comfortable.
It's faster to aim the arrows and all, but it's harder to use sword(and slower).
GC version can even change camera angles which come in handy.
bottom line = GC control is comfortable in general.
3. sound comes out from wiimote and that's really cheap quality. GC version sound comes out of TV which is better quality. Thus GC version sounds better.
4. wii version supports 16:9 widescreen thus it looks cooler~ gives u better view of field.
The last comment I want to make is that Nintendo really doesn't care about graphic because they are so dumb. YET! they make games with such a great gameplay.
1 mistake they made for Gamecube is that they deleted component slot since 2005(or 2004, not sure) and stopped making component cable. It's freaking rare and being sold for $60 just for A cable!
This is why GC version supports 480p, but poor people can't play it with 480p because they don't have component cable.
wii was just released and it has so many component cable from both nintendo and third party. Thus it's EASIER to get a chance to get a component cable and enjoy 480p.
Bottom line = GC and wii got EXACT same graphic, but it's super hard to buy GC component cable. GC component cable = over 60 dollars(Ebay only!), wii component cable = less than 20 dollars.