First, why do I need "/include"??? A language-specific directory on the top level? "/games" is equally stupid.
Oh, and how about /amd64-mingw32msvc, /arm-linux-gnueabi or /i586-mingw32msvc? Won't it be lovely to have them on the top level?
What we really need is consolidation of everything under ONE directory. I'd better move /bin, /sbin, /lib TO /usr if I had my way. Unfortunately, it's too deeply ingrained by now in all sorts of applications.
Think about it for a second. Imagine that you'd have a Linux with /etc, /home, /var, /usr in the top directory. Maybe also /system for sysfs, procfs and runtime directories. Won't it be easier to manage and use?