The FHS has been poorly done for years. For e.g. where is the canonical place for a Web vhost root? /srv/www? /srv/web? /var/www?
One thing I don't like about its filesystem is its insistence that all binaries go into /bin. As a user, I greatly appreciate the concept of having some sort of /local directory to distinguish between files (or just executable in this case) which the end user installed and which are part of the distribution. If you abandon the idea that /bin has no subdirecories, then I could see /bin/local as a viable alternative (although I think I would still prefer a /local folder where that had /local/bin, /local/etc ...).
Also, one thing I think is needed right now is an easy way for users to install programs in $HOME, only for themselves (not system-wide) and without root access. On most distros (AFAIK), you can only do "sudo apt-get install PKG" (or something similar) which installs the package system-wide for everyone, or you can go through the whole configure&&make fun to install a program in your home directory. I'd like to see something like $HOME/bin and $HOME/lib where users can auto-install binaries that only they use.