This thread is a reminder that game players, and to an only slightly lesser extent the gaming press, are largely responsible for turning individuals into superstars and idols. Creating the impression they are god-king tyrants at their company.
Miyamoto has been turned into an icon partly by people who seem to think he personally programs every Nintendo game. And to be fair, partly by Nintendo using him as an external symbol because that's what any company does: it's called marketing.
The real mistake however, is in the public actually taking such things literally. You do not know what Nintendo's internal organizational structure really is, sorry to say. People need a hero/villain. (Especially the villain, when they're busy hating on their favorite company for not doing what they want.)