Oh, for goodness sake, giving a story to a main Mario game is just stupid! We don't need a story. You know why? Because, if there's a story, we're going to be interrupted every few levels with "Oh, Mario, here's some more stuff about the plot". Or every world. The ONLY way I see it working is if they do it like Sonic Colours did it. Have some cutscenes, but make them more comic-relief than earth-shattering. And make it only happen after a boss battle, when we're expecting a break, anyway.
And about Miyamoto, I don't think he should retire or anything like that. I just think he should have less influence on story and narrative in other games. He can make fun gameplay, but I think we know he isn't used to telling a story.
Also, if you actually liked the storybook in the Comet Observatory, that's fine. But we all know if it wasn't optional, we would probably hate it.