Exactly. Which leads to some of the most awful and crazy designs decisions.
Look at the upgrade to 64 bit. In Windows 16 bit days you had the C:\Windows\System directory. In Windows 32 bit, you gained C:\Windows\System32 for your system libraries. In Windows 64 bit you would assume C:\Windows\System64 right? Nope. 64 bit dlls go in to System32 and 32bit dlls go into SysWOW64. WTF?
Same goes with Program Files (32 bit) etc. They are pretty much screwed by legacy.
The windows mobile, XBox, and WinRT guys must feel so much better than having to work on Windows core because they don't have to deal with supporting 17+ years of software still running on their platform.