There are many details that people don't know, I will try explain the simple way possible.
1. Nintendo sold Rare to Microsoft for a good amount, it's not really Rare's fault.
2. Actually Rare is just a shell of the old Rare, many talent just flew off the company, that was the reason Nintendo disposed them.
3. GoldenEye situation is a copyright hell right now, see: Activision has the rights to publish 007 games, Microsoft has the original developers, and I think part of the N64 code is owned by Rare, Nintendo has the rights for GoldenEye 64.
4. Nintendo will not allow to MS publish such a important N64 game.
5. Microsoft will not allow to Nintendo launch a game from its own first party studio (Rare)
6. Activision is hand tied with 007 rights XD
7. There was some rumors back in the day about MS making a deal with Nintendo to release the game in both 360 and Wii, but Nintendo refused, since they have never allowed its own content in other platforms, (Banjo Kazooie, Conker are different, cause both IPs were created completely by Rare)
Is a mess, I know. =P