Perhaps if /usr/local was a normal folder, containing symlinks?
The problem is more related to support you had multiple CF cards, or wanted to run apps from the root/CF/MMC all at once- linking per-app allows you to achieve this.
Also, linking to stuff that has been removed isn't nessecarily a bad thing (for instance we can prompt media re-insertion); the main reason I was thinking to have a single folder that lists all the application startup scripts, is then we can standardise tools to edit er_registry and so on by examining this list.
I'm a big fan as you may have guessed of eliminating the concept of install/uninstall