* Agile practice indicates that experience with users is the best way to keep project on a useful path. Research groups necessarily act without such input, which leaves them prone to going off into the weeds, including producing interesting technologies without a total appreciation for the practicalities, or a clear path to delivering it to users.
* One of Jobs' first acts on returning to Apple was to disband the research group (http://news.cnet.com/2100-1001-203996.html). Why? I would guess because he wanted research to happen in the course of and for the purpose of innovative product development. There you can get the benefit of a user-focused development process, with a defined end result.
* As with any institution (e.g. NASA http://news.ycombinator.com/item?id=1092972), without accountability from strong leadership or users they're prone to unproductive efforts. After all, how do you judge the quality of their efforts? How can you motivate them to strive - day to day at all levels - to make an impact, when they have these cushy unaccountable ivory tower positions?
Or, more practically, what has MSR produced that's active in changing the world, compared to a handful of startups acquired by Apple?