The biggest dissapointment for me was contradiction between de-jure principles stated in Standards of Business Conduct, and de-facto behavior of local management, which in many real-life examples showed lack of human vaues, leadership and responsibility. So, the problem is in the process of selection and hiring of top- and middle-level managers, where company does relatively well in looking into function-specific qualities of candidates but fails to select and hire managers with proper leadership capabilities.
Another one downside is extremely poor work-life balance, when urgent and complex tasks come with very short deadlines, causing many people to work till late nights 5-7 days a week. Declarative slogans that company respects employees' WLB, simply does not work.
And in many cases you can see when some manager might take an exccessive and not realistic commitment (to get promotion for example or award or visibility to upper level), but then after facing difficulties in getting to the target, showing up blaming everybody around and not having courage to take responsibility and acknolwedge his or her mistake.
I saw many talented people leaving MSFT because of the reasons described above, with senior management not making steps to eliminate route cause of the problems. This is pity.
The last but not the least (already stated in some feedback here). Internal attitude towards competition must be different. It must respect competitors.