The most common story I heard when Rare cancelled their XBLA port was that Nintendo didn't own a thing and that Goldeneye's ownership was no different than Perfect Dark, Blast Corps, etc. Seems believable given that it's difficult to believe that development would ever reach the late stages that it supposedly did if Nintendo had any ownership. And contemporaries of it on the N64 that didn't involve Nintendo IP stayed with Rare after they left the Nintendo fold, so there's no obvious reason why Goldeneye should've been any different.
Apparently Activision, the videogame rights holder at the time for this movie franchise, was willing to cooperate with MS/Rare to allow them access to the James Bond license. But they also wanted to protect their relationship with Nintendo and wanted their unofficial blessing before cooperating to get such an iconic Nintendo classic out on a competing platform.
Sadly, Nintendo said that they'd rather Activision didn't cooperate, and that was that (Even an offer by Rare to release the N64 classic on the Virtual Console supposedly didn't change their mind).