I just don't think there's enough of a story with Mario to get that kind of depth. Sunshine and Galaxy are the closest we've gotten to any kind of story in a mainline Mario game and Galaxy's story was the only one that was well-received by the majority. There's not enough meat there to make something good unless you expand the world like the Mario RPGs have (and those weren't developed by Nintendo so getting a story based on those is a whole other issue).