I think Miyamoto's semi-retired as the figurehead of Nintendo. Miyamoto, Reggie, and Iwata were pretty much the faces of Nintendo during the dark times. They had super memorable presentations, but they were also sort of characters and they distracted by being a cult of personality. Could be that they just want to move forward with younger guys.
Just to add on this, Miamoto started working for Nintendo in 1977, so over 40 years ago. I'm pretty sure that by now, he's mostly just overseeing the training the next generation of programmers at Nintendo, teaching them some tricks, and come up with some ideas once in a while.
In other words, I think he will soon retire entirely from the business. After all, he's 66 years old, that's a proper retirement age already.
The Nintendo eShop rating Thread: http://gamrconnect.vgchartz.com/thread.php?id=237454