I don't think this is comparable to the Zelda case, Miyamoto adamantly (and wisely) refuses any sort of focus on story, at all, in Mario or Zelda. I remember Koizumi had to sneak the storybook thing in Galaxy under Miyamoto, or he would had cut it.
If Metroid was his baby no story would touch it, thats for sure. And it's funny because RPG need story more than action games, however whatever little story is needed for Zelda comes from the gameplay design alone, and not some crazy or fan-fiction like idea in someone's head.