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.
You know it deserves the GOTY.