The real troubles with MS platform are: .NET troubles (heap fragmentation, long term unfixed issues), troubles with scalability (try to read about removing big kernel lock in Windows 2008 and W7 from Microsoft itself), NTFS fragmentation issues, no real real-time support (requires patching Windows kernel by third party), inability to hire somebody who is able to fix issues in the Windows kernel, inability to hire somebody, who is able to audit whole/part of the system. The big problem is that there is only ONE firm, who is able (or claiming to be) to fix and patch the core of the operating system.