In the HD version the gamepad makes it easier to navigate between items and the stamps are another cool collectable that don't get in the way of the original game, plus it looks better. My biggest gripe with it is they mirrored the world for hero mode, I wish they wouldn't of or at least let you choose if you wanted it mirrored.
Cube. Really don't like those stamps and amiibo stuff, and the graphical upgrade is pretty minimal. especially if you compare it to the Cube version on higher resolution.
Also irked me that they closed off that area in Ordon where you could actually catch ordon catfish. No reason to do that honestly.
The GameCube version, I love it as an original. Wii is a bit of a pet peeve for it being backwards while the Wii U was like a slap in the face from Nintendo because they didn't do very special to it with only the Wolf Link amiibo being the only thing redeeming