Do you mean the byzantine directory structure for system files? The default of installing to "Program Files" doesn't seem too unusual, although adding "x86" bit seems unnecessarily complicated for a typical end user. Same with the rest of the standard directories that people use most often.

The directory structure for system files is bad, but that's true for Unix-derivatives too. Unix has /bin and /lib, /sbin, /usr/bin, /usr/lib, /var/opt, etc. Different versions of Unix have different ideas of what belongs where. Even different flavours of Linux have their own ideas.