Mods shmods. Makes me think about a DLC of additional traits and abilities for custom factions. 20 of each would be nice.
Then, just to keep with the Extremely-Demanding-of-Devs theme, another DLC to get the AI able to build a custom faction with coherent flavor text pulled from a box-o-blurbs that are tagged to associate with traits, abilities, personalities, and other blurbs.
Could be much stronger replayability boost than the map generator, but probably ludicrously time-consuming to code...