The order emulators appear in EmulatorStation is the order they are in the es_systems.cfg
If es_systems.cfg is missing in ~/.emulationstation/
you can copy it from /etc/emulationstation/es_systems.cfg to ~/.emulationstation/es_systems.cfg
To make Mega Drive appear first, edit es_systems.cfg and move
<system>
<fullname>Sega Mega Drive / Genesis</fullname>
<name>megadrive</name>
<path>~/RetroPie/roms/megadrive</path>
<extension>.smd .SMD .bin .BIN .gen .GEN .md .MD .zip .ZIP</extension>
<command>/opt/retropie/supplementary/runcommand/runcommand.sh 4 "/opt/retropie/emulators/RetroArch/installdir/bin/retroarch -L /opt/retropie/emulatorcores/picodrive/picodrive_libretro.so --config /opt/retropie/configs/all/retroarch.cfg --appendconfig /opt/retropie/configs/megadrive/retroarch.cfg %ROM%"</command>
<!-- alternatively: <command>/opt/retropie/supplementary/runcommand/runcommand.sh 1 "/opt/retropie/emulators/dgen-sdl/installdir/bin/dgen -f -r /opt/retropie/configs/all/dgenrc %ROM%"</command> -->
<!-- alternatively: <command>export LD_LIBRARY_<path>"/opt/retropie/supplementary/dispmanx/SDL12-kms-dispmanx/build/.libs"; /opt/retropie/emulators/dgen-sdl/dgen %ROM%</path></command> -->
<platform>genesis,megadrive</platform>
<theme>megadrive</theme>
</system>
to the top, right under <systemlist>
in the es_systems.cfg
Hope this is understandable. I’m totally new to Linux, got my RPi 2 days ago and trying to write this with a crappy wireless keyboard on my RPi. ;)