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. ;)