Sort of a shame that this is true.
Some people always encourage Nintendo to buy more studios with their big profits, but I really don't think that's a good idea. It has rarely worked out for them in the long term.
Retro should be announcing a new project soon, and whatever it is, I guarentee it will now be looked at with skepticism.
"[Our former customers] are unable to find software which they WANT to play."
"The way to solve this problem lies in how to communicate what kind of games [they CAN play]."
Satoru Iwata, Nintendo President. Only slightly paraphrased.