I'm approaching (not entering yet because I still haven't got a purse upgrade and I'd like one of those before going for phat loot again) the 4th dungeon right now in the GC version, aside from the camera controls being limited in comparison to WW (only two zoom levels, lots of areas with forced camera angles you cannot change) and the slower aiming which makes some enemies a pain to deal with (you can lock on but sometimes you want to snipe them from outside your lock-on range) I don't think there's much wrong with it. There's occassional slowdown but it only seems to happen in transition areas where not much is happening anyway. You only have two item slots (Midna takes up Z) but item swithing is fast enough and you don't need to switch that often. Fishing is pretty simple from what I've seen, the movements mimic what you do with the Wiimote but I haven't done much with it since I really don't care about fishing. There's no clock to show the day/night cycle which can get annoying if you want to get into some stores (some are open 24h but some are not though I've run into the wrong time annoyance only twice so far) but I think that's not version specific. BTW, claims that you can't do the spin attack without charging are wrong, just do the circle motion with the analog stick if you don't have the time to charge it. This may need some progress in the game to do, I haven't been able to pull it off at the start (though that may have been me not rolling a full circle) but it worked later on.
Granted, I haven't played the Wii version but so far the GC version seems to have no big issues. Gamespot gave it 0.1 points more than the Wii version. And Midna has her right eye visible which means you'll understand why Bill needs Gannon Banning.
BTW, with the dpad being used for item slots, what brings up the map and item screens on the Wii?