Legal issues are partly why. Mother 3 (and Earthbound) have songs directly pulled from other sources and other references that far too closely resemble other copyrighted material for it to remain in the game.
But I think there has to be more to it than that. You can't even find Earthbound (Mother 2) on the Virtual Console in Japan, where the legal issues that prevent it from being released elsewhere are not as prevalent. If it was just a matter of altering the legally questionable material, they probably would've done it by now. I think it might have to do with the dark undertones present in the series. Earthbound is mostly a spoof of American culture and Mother 3 has some pretty sinister underlying themes to it, themes that sharply contrast the bright, colorful art style. You can't change or remove these themes because they're a major part of the story and general mood of the games. It's just a theory of mine, but there has to be something inherent to the series that's convincing Nintendo to stay away from it outside of Smash Bros.
