Since 12.04, when additional software is installed, Ubuntu software center puts an icon in the launcher, representing a .desktop file in /usr/share/app-install/desktop/. This desktop file is not "overruled" by a (possible) local .desktop file in ~.local/share/applications. My question is: Why is the initial icon (.desktop file) put there, and is not the default .desktop file used that is located in /usr/share/applications?
Because that is how Ubuntu was designed. When you install an app from Ubuntu Software Center, Ubuntu puts an icon for only the user who installed the app.