Here is how I understand the current system is intended to work:
1. /sbin for binaries for use by root that must be available before the system is fully brought up (and for an emergency copy of the Bourne shell), which should all be linked static.
2. /bin for binaries for use by all users that must be available before the system is fully brought up. These may be linked dynamic.
3. /lib for libraries which are needed for binaries in /bin to work, and for kernel plugin modules in /lib/modules.
4. /usr/sbin for other binaries in the base system to be available to root only.
5. /usr/bin for other binaries in the base system to be available to all users.
6. /etc for global configuration files used by the kernel and the base OS.
7. /opt/PACKAGE contains a full bin, etc, lib etc. folder tree for every non-base package (I would put almost everything here, including X Window in /opt/X11/bin etc.).
8. /home as the base for all user folders.
(Scripts and binaries are not differentiated in this system.)
I think I would be prone to do a cleanup of the system to isolate everything into some form of the above. Just my opinion.
-uso.