I suggest further decentralization of 'moddable' images (like flags and races, which already have their own separate folders), and text stuff like lists of names, surnames, ship names, system names, race names and ranks. Something in particular I'd like to mod myself are some of the icons present on the System Map: icons like the ones of the Task Force, Events and Intelligence on Alien Classes* windows make little sense, for instance. In fact, most could be improved in some way.
Another, smaller suggestion I have in mind is referring to officers using "they" and "their" when applicable, given you need to be genderless due to the presence of female officers. That is, unless you can overhaul the system to use he/she and his/her properly, but I'm guessing that's quite more complicated.
That's all I can think of right now.
*This button seems redundant as it leads to the same place as the Diplomacy one does.