But there's litte separation between important system settings and less important user settings.
So, how much separation do you need? System settings vs user settings tend to be in different parts of the registry namespace, different parts of the namespace tend to be separated in different hive files, and you can have per-key ACLs to prevent users from screwing things around. At least on my w2k3, the defaults permissions aren't completely braindead. either. Normal users aren't allowed to touch many of the things they shouldn't, and if you're always in as an administrator it's your own damn fault if you screw the system.