Didn't we get multiple versions of LoZ and SMB after they were part of compilations?I also prefer Prime 1 over the other two (though I never played much of 3) but I doubt even Nintendo could get away with selling it on its own unless it was either budget priced/digital only or if it was a full on remake.
Like others have said, they were bundled already on the Wii. There's no reason to separate them.
Super Mario all-stars---->SMB on Wii, Wii U, 3DS, NES classic
Zelda master quest on GCN-----> LoZ on Wii, Wii U, 3DS, NES classic
The argument put forth by some in here that the Metroid Prime games can't be seperated and resold seperately because they were sold together on Wii holds absolutely no water.
In fact, if you go even further there is ample precedent for actually doing a remaster of game with all new graphics, then going back and rereleasing the original shitty looking version.