Miyamoto isn't a "problem" per se, its the way that Nintendo uses him that is.
As has been stated, he oversees software development at most if not all of Nintendo's software develop teams. He gets to shoot down ideas that he disagrees with, and greenlight ones that he does. I bet a lot of interesting ideas that could have been made were rejected because Miyamoto disapproved of them.
There is no doubt that Miyamoto is a genius software developer, and that's where Nintendo should be using him. Put him in charge of his own studio and allow him to develop his own ideas as he chooses.







