Shigeru Miyamoto isn't the president of Nintendo. That's Satoru Iwata. Shigeru Miyamoto is just the creator/creative director for most of Nintendo's key franchises like Mario, Zelda and StarFox.
This whole talk about him retiring has been circulating the net since before Skyward Sword was released. When he does leave Nintendo I wish him the best of luck. But for now it seems like some of the projects will have at least a little bit of involvement on his part. It's nice that he's making it a gradual change instead of ducking out suddenly.