Wii
+: wide screen, pointer controls (3rd shoulder perspective btw instead of 1st person), sword swinging
while walking, no frame rate issues (GC version has a few locations with a low frame rate)
- : no camera control beyond centering with a button press (like OoT/MM on N64), mirrored visuals,
swinging just replaces the B button
Back in 2006 I was outraged about how bad the controls were implemented. There are so many way to implement camera control without a 2nd stick (e.g. via pointer, Nunchuk or D-Pad).
Even after the re-release on Wii U I still don't think there is a perfect version out there. Instead of fixing the Wii controls (e.g. vertical and horizontal swings via Wiimote is no problem - even without Motion+), they got rid of them completely, which is totally fine, but why not offer both options (like in RE4 on Wii)? Furthermore, the visuals actually look better on Wii in my opinion because the Wii U version does not add polygons or grass (the sharper textures just don't look better in my view).
They also made small changes to the content of the game, e.g. Wolf Link has to find fewer orbs. I don't view them as improvements but at least they are not as bad as in the Zelda MM remake for 3DS.
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It amazes me how ports like TP and Okami on the Wii could exist with no classic controller support. You're removing traditional pad input from the game when the system already has a traditional pad. Just, why? How hard is it to just copy-paste PS2/GC controls onto the pro controller like Resident Evil 4 and Black ops did?
Wait, I think RE4 supports Wiimote and GC controller, while CoD Black Ops and MW3 support Wiimote and CC. Goldeneye (and some other games) support all 3 though.