Nintendo published the original game, for rare, so they both have a stake in the game GE64 as an IP.
Microsoft now owns rare so it also no has a stake in the GE64 IP
In order for a GE64 game to come out, rare, MS and Nintendo would all have to come together on an agreement which is Extremely hard to do, especially since they tried (completed an HD remake for 360 similar to PD) once, it failed as nintendo wanted it to be a wii exclusive.
Lets say MS, rare, and nintendo COULD get an agrement, they now have a new hurdle, they gotta talk to activision since they are the only ones who can currently make money off of the bond IP in video games right now... activision would want a slice of that pie thats already getting split up quite a bit.
its a case of legal grid lock no one is going to be able to remake and release a remake of goldeneye 64 and make money off of it. thats why the Goldeneye on wii was sort of a reimagining rather than a straight remake. and thats why we are sort of in the eye of a legal hurricane relatively safe, but still in a tricky situation if the huricane changes course, or we step to far in any one direction hehe.