I vote for Lua, personally, since it’s got broader applications in the modding and emulation scene. Emulators that support external scripts generally support Lua, sometimes exclusively, and in fact Lua is what Nintendo uses on the Virtual Console emulators for real-time modifications (e.g. Pokemon Yellow VC changing Jynx to be purple, dimming the screen during flashing animations, all the game-specific stuff they had to do for the N64 VC on WiiU/NSO etc). There have even been, for better or worse, AAA games done mostly or entirely in Lua (looking at you Sonic '06).
Additionally, there are a few Lua tools already written for the GBAFE scene, including Stan’s very own proc tree display script and MisakaMikoto’s world map routes inserter. I think there’s practical value in keeping down the number of languages one has to know to do a hobby. There’s less overhead from having to install a whole new environment and compiler just to edit one line in one script.
Finally, purely personal bias, but I’d rather not have to use JS in my hobbies when I usually use it in a work context