That is certainly one problem Windows has. It's also not really orthogonal (I'm looking at you, registry) and doesn't strive for simplicity or elegance like Unix/Linux tend to do. (Why the user folder is so ambiguous and mysterious before Windows 7 is beyond me.)
If Eric Raymond is to be believed, another problem is that it has no unifying concept, a la Unix's "everything is a file" or Apple's "make the GUI simple and focused".