Mod load order controls
Simple (I think?) feature that would help the modding community tremendously - just give us a control on the modding screen that lets us choose the order in which the game loads mods. Drag and drop order, like various existing mod managers, maybe? Dunno, I'm not picky about the exact implementation.
If doing UI shaboingery isn't on the cards, even just ensuring that it always loads mods in a predictable way would go a long way.
In any case, this would help dramatically with both compatibility between different mods (including making debugging more consistent) and with mods that want to split up into submods. It'd also enable the possibility of a community of third-party compatibility patches between otherwise conflicting mods, as has developed in other healthy modding communities like Stellaris or Fallout.