While Nintendo has a number of popular faces, it's hard to beat the presence of Miyamoto -- he's a living legend. He cares a lot about games and gamers, and he has an incredible history that easily qualifies him to take the helm.
We can start with the fact that Miyamoto has been with Nintendo since it first got its feet wet with video games -- six years before the 1983 release of the Nintendo Entertainment System. Here's a sampling of some series Miyamoto has himself created: Mario, Donkey Kong, The Legend of Zelda, Star Fox, and F-Zero. To create one of these now iconic series would be impressive, but he created them all, and then some.
Given his amazing contributions to Nintendo, and his likability -- not to mention his ability to captivate crowds -- he seems like the perfect fit for Nintendo CEO. That of course assumes he'd even want the position, but I think it's safe to say that the company would be in great hands if he were to take the position.