Microsoft have lagged behind in a lot of key areas when it comes to system administration.
Windows still doesn't have a decent equivalent of apt or yum (that I know of), the basic command prompt is still shit, PowerShell's a bit of a joke in my opinion, the default editor is still Notepad, and my options for administering a web server are still either a shit GUI or a shit XML file format.
I don't know why they haven't solved any of these problems as they've been the same for over a decade now. It almost feels as if no one is working for them at times.
Oh yeah and ad hoc management of filesystem ACLs still sucks too, that's one of the shittiest dialog designs you'd ever see.