Emulationstation scrapes games based off of the platform value in the es_systems.cfg which is currently listed as Megadrive. If you wish to change your theme from megadrive to genesis as well as the scraping, you need to make your megadrive system look like this:
/etc/emulationstation/es_systems.cfg
<system>
<name>megadrive</name>
<fullname>Sega Mega Drive / Genesis</fullname>
<path>~/RetroPie/roms/megadrive</path>
<extension>.smd .bin .gen .md .zip .SMD .BIN .GEN .MD .ZIP</extension>
<command>/opt/retropie/supplementary/runcommand/runcommand.sh 0 _SYS_ megadrive %ROM%</command>
<platform>genesis</platform>
<theme>genesis</theme>
</system>