Hi Florian, I'll have to check the details but in general you can set the default system connection in the admin file (with NWBC 5.0 the SAP UI Landscape administrator configuration file replaces former NWBC configuration settings for system connections and search providers in %ALLUSERSPROFILE%\SAP\NWBC\NwbcOptions.xml). Then hide the system selector on startup.
see also here:
http://scn.sap.com/docs/DOC-62417
Regards,
Sandra