avoid a global registry for local apps
One of the biggest problems with having a single global registry like in Windows is that if you do a clean re-install of the OS, or a from-scratch install of an upgrade, you lose everything, including applications you may have downloaded and installed separately.
One of the nice things in Unix is that you can have /usr/local on a separate partition/filesystem, and that way when you do a clean re-install of the OS, you can avoid formatting /usr/local, and so continue using all your existing applications in that directory. This is possible because the configuration information for the applications was stored on the same filesystem as the application itself. If some important configuration information were to be stored in a "global" place (e.g., in /etc), then this advantage would be lost.