I wonder what is more likely in our lifetimes - a sane Linux filesystem layout, or viable fusion power. Honestly I'm not sure.
gobolinux - http://gobolinux.org/ - has had a completely different filesystem layout, for many years. It's languished in the past few. archlinux has for a couple of years symlinked /bin, /sbin, and /usr/sbin to /usr/bin, and /lib, /lib64 to /usr/lib https://wiki.archlinux.org/index.php/arch_filesystem_hierarc... If you make your own linux distro from scratch, you can get many of the open source pieces of a linux dist…
That's the one I was trying to think of! Yeah, they solved the directory problem. NixOS solved the packaging problem. Little projects doing what they can to fix the UNIX/Linux mess.