My favorite somewhat-rethought OS is GoboLinux, which is not as different as Plan9 since it's basically just Linux, but it totally throws out the traditional Unix folder hierarchy of /bin, /etc, /var and so on. I also like the simplicity of classic Mac OS where you install a system extension by just copying it to a special folder and you uninstall an app by just deleting it (which sort of works with current macOS but apps still strew preferences all over the place).
Believe it or not, there have been several attempts to bring that kind of application management simplicity to Linux: ROX AppDirs, GNUStep's AppBundle implementation, Klik, and AppImage to name a few.
They have all been rejected by the community at large, sadly.
Yeah the usual argument is that package managers make worrying about the tidiness of the file system unnecessary. But on Linux at least it just never really works out.
