I don't know if it was their idea from the start, but MSR is hugely different from other companies' R&D. They operate more like a university. Researchers are free to work on anything they want, without consideration to whether it will directly effect a Microsoft product or not. It is one of the few places left outside academia where researchers can do basic research in computer science.
I have no way to know if that's right or not, but I'm willing to concede that it's right. I wonder if the problem was that they accomplished nothing of value or if they did actually come up with great ideas, but the non-R&D management above them squelched them. In any event, Microsoft has always struck me as a reactionary rather than visionary, which is exactly why they are pursuing their current strategy of trying to become major players in phones and tablets. Microsoft just waits to see where everybody else in the industry is going and then they follow them and try to pretend that they were there first. In the past that worked pretty well on the PC side of things, but consumers understand phones and tablets enough that they can't get away with that in those areas.