Mnemon: Well. As Linux (and Mac OS, in extension) proves: An Operating System does not need a registry. I am fairly certain if Microsoft could they'd drop that thing.
Problem is increased because programs really do tend to overuse the registry. As said above .ini's / .conf's are nearly always the better solution. The average normal user will (hopefully/usually) never touch the registry or .ini/conf.. The more advanced ones should really know where there programs are installed and hence find those .ini / .conf if they really want to play with them.
I.e. I don't see the argument that a central registry is in any way useful, especially because everything adds to it. If you do not know what you are searching for precisely, it can quickly turn into that haystack / needle thing.
Although, Mac OS
does have a registry of sorts, the system-wide, and user-specific library folders. Sure it's split up into hundreds of files instead of half a dozen, but they're equally left where they are when the user removes the program.
Of course, the user in that case don't need admin privileges to edit his own branch of the application and system settings repository, and if a non-admin does a mistake the worst they can do is fuck up their own account. That is, I feel, really the worst design flaw of the registry so far, you need admin rights just to open the app, even if the only settings you're about to edit are ones specific to your own account.
Ditto Linux and other Unix-likes. System-wide settings in /etc/ and user-specific in your home folder (most often hidden by starting the file/folder name with a dot)