Koizumi doesn't write stories of the type that "Nintendo has fallen behind" in, not really anyway. And BoxBoy just came out last year.
And you're really overselling Miyamoto if you think he's also going into projects and tells them to tone down the worlds. In fact, I don't really see this "lack of interesting world design" in any recent projects.
On writing, the type of writing that Nintendo has fallen behind in is simply good writing. Compare Galaxy's storybooks with Rosalina to where the series is currently. Compare the narrative of Majoras Mask to where Zelda is now. Fire Emblem too. Clear regression in quality of writing.
Lack of world design in the sense that they have taken the approach of simplification over improvement. The most obvious example being the hub worlds in Mario being removed for a simplified map instead. Zelda and Metroid being other obvious examples.
As far as overselling Miyamoto, yes he has had very little actual development involvement over the last several years, but a number of weird software decisions, and software policies, can be traced back to him through interviews.