The Rare deal is one of those deals that IMO everyone lost on.
Nintendo could've sold a fair amount of new Banjo-Kazooie, Killer Instinct, Perfect Dark, Viva Pinata, Kameo, Diddy Kong Racing, etc. games on the Wii and DS with the much larger userbase and filled a lot of holes in their release lineup, probably allowing them to launch the 3DS and Wii U much more strongly as well and preventing some of the headaches Nintendo has had the last few years.
Microsoft really got little/no benefit from the Rare acquisition and alienated most of the staff in the process.
Rare obviously became a shell of what they used to be.
I think Nintendo should've just bought them and reorganized the studio a bit to refocus themselves on games that weren't so large/bloated.