/setup is useful to restore the VS settings to their original state.  If you have, for instance, packages that failed to load and you clicked the button to disable them from loading in the future, you can get them back again with the /setup switch.  The original problem that caused the package to fail to load may or may not have been corrected so you may need to correct that before all packages load correctly.

This is similar to /ResetSkipPkgs, but also gets newly installed packages resource info completely registered.