In response to what Wired had reported yesterday, Nintendo has denied the assumption that Miyamoto would be stepping down from his position as head of Nintendo.
Nintendo said that there was a bit of a misunderstanding and that Miyamoto is passionate about training the younger generation. At the moment, Miyamoto has no intention of stepping down.
As Miyamoto said, "What I really want to do is be in the forefront of game development once again myself. Probably working on a smaller project with even younger developers."
Fans of the Nintendo brand should not be concerned and instead should keep on playing through The Legend of Zelda: Skyward Sword.