They don't have to make the game again to put it on virtual console, it's just a transfer of the code.
Rare was bought by microsoft yea, but they still make DS games.
The only company they have to go through is activision(or is it EA now?), they have bond game rights, MGM only has movie rights and Rare has nada.
Games like Conker/Banjo would likely be harder to get because Rare created the characters for it and not just developed it + it's on xbox now.
Nintendo can release any game that was made for the original console but they can't change anything. Some games would require royalties for the use of the ideas/characters/etc.