Nuked-MD MegaDrive core has support for EEPROM saves! Game changer. I haven't tried it yet though.
EDIT: I tried Micro Machines '96 and NBA Jam TE. Both work! Good times!
However NBA Jam wouldn't work until I did the "AutoStat™" feature fix lol - https://tcrf.net/Bugs:NBA_Jam_Tournamen ... _(Genesis)