Miyamoto is great, but really he wasn't that involved with games like Super Mario Galaxy 1 or 2 which were developed outside of the main EAD group in Tokyo. In fact, Miyamoto was initially against ideas like the orchestral soundtrack in SMG, thankfully EAD Tokyo got their way.
Kid Icarus Uprising is the best game on the 3DS too and his involvement with that was little/null. The Galaxy games are the best games on the Wii.
Nintendo's greatness is not tied to one designer, they have many, many designers that are incredible that simply aren't as publicly known.
I would say the best Nintendo games of the last 4-5 years are Super Mario Galaxy 1/2, Xenoblade, Kid Icarus Uprising, and Donkey Kong Country Returns ... and Miyamoto wasn't hugely involved in any of those.
Nintendo is not one man. It's a development culture. Look at the level design for NSMB2 ... it was made by a younger "B-team" quickly assembled and developed in about 9 months time, given a "Mario crash course" in design. And the level design seems spot on to previous Marios. So clearly Nintendo is very good at grooming young talent.
