You are right Halbred, Metroid Prime was worked on with the help of Miyamoto. Nintendo has for the most part gotten the best out of developers they work closely with (I do not mean those instances where they just handed a franchise off to a developer and said "Go for it!"), Metroid Prime, and Eternal Darkness being their biggest examples. Even Geist, while it appears Nintendo had some influence, still is a quality albit flawed title.
Now if Team Ninja was handed Metroid and Nintendo wasn't working that closely with them, I'd be worried but as it is, I'm not because Nintendo has an amazing track record for co-projects. They seem to have an eye for getting the best out of a developer in that arrangement, even possibly changing them for the best (retro) or at the very least maximize the unique talents of a developer while providing guidance (Silicon Knights).
Team Ninja has had signs of brilliance, especially with their 3D Ninja Gaiden things. I expect Nintendo to get the most out of them as well.