I can't find the exact quote, but I believe someone at Nintendo (Maybe Iwata) said they don't normally buy other companies unless it's one they feel has generally similar corporate philosophy and are willing to work under Nintendo. Otherwise they may simply buy a name, and the talent may jump ship in a hostile takeover.
EA has done this several times. Bought out a company and tried to bend it to their will only to alienate the people who made the companies what they were. In Retro Studios case, they were struggling to get something off the ground, so they were pretty happy when Nintendo offered a chance to revive the Metroid series.
It's possible this whole thing with Fatal Frame IV might have something to do with them trying to hire new talent. Kind of like what did happen with Monolith Soft. Nintendo was Disaster's publisher since that game's announcement and eventually they bought Monolith after they decided they'll work well together.
