I think that Microsoft should be more open on the inner workings of the operating system. I mean, with other operating systems you know which files are exactly needed for a minimal installation, which is the kernel, where are the settings files and what they mean, which files are the drivers and when they will be loaded. Plus, you can open up the settings files and change up the order of loading drivers or tune various documented settings as required.
In Windows, everything is obscure. And even when there is information on how to change some features considered not for the average user by Microsoft, it is usually by chance that you find out on the Internet and not by official means. Does anybody, I repeat anybody, even a Microsoft employee know what each file under c:\windows does and why it is there and if and how you can aulter the directory structure of a Windows installation? (Without breaking something that is.) Plus, everything is hidden away in that huge registry and nobody, even Microsoft employees, knows what the various keys and values stand for. There is no official and easily accessible resource that documents everything. Compare this to the settings files of other operating systems and how one can virtually install Linux on any removable media (like on cds) and in a directory structure of his own making and not always have to stick with c:\windows\system32, etc, etc.
If Microsoft was open about the Windows internals and if MS wanted to really help the administrator, there would have been a standard and visible way of configuring the operating system. All registry entries would have been documented. The roles of each file would have been apparent. And there would have been a simple way of creating your own Windows installation, adding your own software and components as needed. Imagine how fruitful that would have been for corporations who might like to customize their Windows installations, like install part of the os on a server, ie. install some not frequently used Windows accessories on a server and keep the files that are used more often on each client. XP embeaded already offers this componentised installation features, so the problems are not technical. Also, if Microsoft might fear support or competition by allowing more customization to the os installation, then it could limit this ability only to corporate or volume license customers. But many flavours of Unix are already very customizable, (they might  allow you to install part of the os on other computers for example), and they do not face such dilemas. They do not worry about combetition for example, this such customisations make the operating system more useful and thus more appealing.