Thanks Florian :-)
Today I solved the problem with an older RetroPie-script and used the commands manually:
cd /home/pi/RetroPie/emulatorcores/
git clone git://github.com/libretro/Genesis-Plus-GX.git
cd Genesis-Plus-GX
make -f Makefile.libretro
And then just change the command-line in es_systems.cfg and the Mastersystem roms working great! :-)