Most people will only get one version--if they have a Wii chances are they got the Wii for Zelda. If they can't get a Wii but have a GC they'll likely get the GC version.

I haven't played much of the GC version, but playing that after completing the Wii version felt slightly like a downgrade. The biggest thing for me was the spin attack--after being able to do it instantly on the Wii it felt so cumbersome to hold down the A button.

However, the fundamental differences between Wii/GC versions can be compared to the DS vs DS lite (where the Wii version=Lite, GC version = Original DS). While the Wii version has different/improved/enhanced features, the actual game itself is the same. They're different enough that it feels different when you play it (I felt kinda dizzy running around Hyrule field, everything was the wrong way), but as far as the story and everything else related to the core game, it's the same.

Wii version has the advantage for me, more for the widescreen support and instant spin-slash than for the long distance targeting. Though if I see the GC version in the bargain bin in a while, I'll probably pick it up. By then, Wii's map layout will be fuzzy in my memory and I won't be so confused when I play.