When it comes to Ganon, another luigifcation is all that's really needed. Change up a couple of his regular moves, and add in a new special or two, and you've pretty much got a non-clone there. In any case, at the time of Melee, I think that Ganon only had about one real appearance, so its actually somewhat logical that he turned out the way he did. Plus, there is the fact that he was last minnute at the time. In all, the only thing I really want to see redone with his moveset is him having the magical rebound ball as one of his specials.
Oh, and in terms of Metroid music, while I agree that Magmoor Caverns music should be in the next game, I'd also like to point out that it, much like the Norfair music, isn't really something for fighting. (Actually, the best Metroid "fighting" music that has yet to be put in, is the Rundas Battle, imho)