It sounds like the Windows registry is an ad hoc, informally-specified, bug-ridden, slow implementation of half of a filesystem. (Amazing how Greenspun's Tenth Rule can be slightly adapted and apply to so many different situations)

If you should find yourself creating an ad hoc, informally-specified, bug-ridden, slow implementation of half of X, stop! Throw it away and use X instead. You'll save yourself and everyone who has to interact with your system a whole lot of grief.