I mean, if you take away the WiiWare and its ability ability to not only download and play mega man 9, but Mega Man 10 as well, and the Virtual Console's ability to play Mega Man 1/2/3/4/X, all the Wii is good for is playing Brawl or Gamecube games such as Mega Man Anniversary Collection and Mega Man X Anniversary Collection or Melee.
Smash 64, Ogre Battle 64, Paper Mario and Mario Tennis are the only reasons to ever play your 64, but you can download those to the Wii. Ocarina of Time, should be with the master Quest on the Gamecube version, so yeah.
Anyway, I understand why you are so confused. You are correct, the Wii is superior to both the 64 and the Gamecube due to backwards capabilities and Mega Man 9 and 10.
The SNES and NES are vastly superior in gameplay, control, concepts, music and dare I say graphics to the 64 outside of a few games that weren't blurry and craptastic. I can't say the same with music in the gamecube, but the rest is mostly true. Bless you Paper Mario. Also, some of the best games of those systems aren't available on VC, though after this argument, I can't say that the Wii is worse than the SNES/NES so it will be held to the highest esteem with those grand systems.