As crazy as your post is, I don't get why Nintendo doesn't just think up some different stories for Mario.
First I think Game experience and Gameplay is more important than story (but also depends what your focus mostly are in games).
I don't love scenes in games, I even hate it when i can't skip it, just because i personal want to exp. it when playing. For deep stories, i'll prefer to watch movies instead.
Second, I don't like spin-off stories, Bowser is the boss. They could get another story, it isn't diffecult, but it wouldnt be a real mario game anymore.
Same for zelda, i always want Ganon as boss, most movies also work like that.
Other games:
Castlevania -> dracula
Metroid -> mother brain.
For example, i don't want a terminator movie to remove Arnold bots and replace it with transformer, thats what you ask.
This mario has a whole different story, only the purpose by saving someone has been the same (so far we know).