Considering his impact on gaming, period...I think that as a nice tribute, Nintendo could offer a few of his older games to the other systems.
1. to honor him by allowing the largest possible audience to play his creations 2. from a business viewpoint...some games they could offer would just be pure profit on all fronts
As far as how it would run...Nintendo would probably try hard to keep his legacy, but ultimately change to something that they are comfortable with, because he would not be coming back to aid. --- I think I'm indecisive, but I'm not sure. Disco lives forever!
Miyamoto himself is not doing much directly in the company at the moment, so losing him wouldn't lose a key talent in some important project at the company.
Most Nintendo designers respect Miyamoto greatly. Just because he's dead does not mean his influence on them is gone--they will try to live up to his expectations. --- "Why do ppl say Steam/PC has DRM? The only thing steam does is prevent piracy, and there's nothing wrong with that." - Oil_Rope_Bombs