Frankly, that's for the best for both Nintendo and the fans.
Nintendo is in dire need of fresh meat in management to actually arrive in the present. They are finally doing things right with the 3DS and its online capabilities (took them only six months) and I hope they dang sure learnt their lesson that you need games for a console to sell. GRAH.
In any case, Miyamoto, as awesome as he is, appears to be quite... conservative, at least when it comes to business. So letting him return to the field he's both best in and most comfortable with seems like the best idea Nintendo had in the recent time. I, for one, can't wait for him to come up with something that might very well turn into a franchise that'll live through the next 30 years.