To me, that thing seems like an utter mess, at least most parts. Some are pretty organized (.NET and GAC-Folders), but most of the others (System32) are not. Wouldn't it improve the general developer productivity if they cleaned it all up? In general - I don't know why they didn't stop that folder becoming a huge mess, and why they don't take any efforts to reduce it. (Win 8 Settings App sits in System32 while Store sits in Root directory, iirc) FHS isn't perfect, but it's far better than that...