It would be interesting, but I doubt it. After other M, they need to be extremely careful about what they do with 3D Metroid, and allowing a 3rd party studio to do it is not the safest thing. Yes, Samus Returns was made by a non-Nintendo company, but it was just a remake of a GB game. Metroid Prime 4 will be much much more important.
If Nintendo's being so careful, why is anyone but Retro developing it? Not to say only Retro could do a good job, but I don't think Nintendo is actually putting a lot of attention into the care of the Metroid IP judging by Federation Farce.
Edit: forgot to say, @OT, I thought Bethesda said Nintendo approached them directly about Skyrim. I doubt there's any secret agenda here, Nintendo is trying to build 3rd party support just like any new console. Bethesda might be an interesting pick for a new Metroid, though.