Hopefully he's been grooming a successor to at least carry on the idea.
After watching a bunch of E3 stuff, especially concerning Super Mario Maker, it seems they have plenty of people in top positions of the company that are all likeminded in this heart for games to remain foremost products of genuine passionate human creativity for the purpose of fun and inspiration.
They have good people there, most of whom got there from humble beginnings deeply rooted in the creation of games, just like Iwata. I trust them to select someone who is at least all about the same principles, even though anyone will have some big shoes to fill, shoes that even Iwata faced constant challenge to fill.
That said, talk of Miyamoto filling in made me think of how he must be dealing with this. He seemed like a very close partner and friend to Iwata. It is hard to imagine him crying, but I can't imagine even the bright and whimsical Miyamoto smiling through this. Thinking of how he must be affected adds more perspective of the loss of this wonderful man as a person rather than merely his role or icon.