Are all races functionally identical in terms of having a large "population" of generic, equivalent entities, and constructing large mechanical ships that all function essentially the same way? Are all races equivalent in terms on industry and research and such?
For example, consider the Zerg from Starcraft.
There are no general Zerg citizens, other than perhaps drones, but there are many different breeds.
Zerg-like "research" in FO would probably function significantly differently than standard science-based research of human-like races... I belive the backstory of the Zerg involves them finding various species around the galaxy and mutating them to fit a niche in the swarm. This could provide an interesting alternate game mechanic for Zerg research. Pehraps biodiversity on a planet would be much more important to a Zerg-like race's research than just population and planetary focus.
Zerg-like "ships" are living things, which could be set up with different "growth" mechanics in game than other races that "build" ships. Zerg-like ships would presumably also have different characteristics / advantages / disadvantages compared to mechanical ships. Maybe grow over time, so you don't need to keep replacing your hulls with newer bigger models. Maybe they self repair.
I'm sure there are lots of other issues that different types of races would have that would be horrible to balance, but would be great for game variety and new play styles and mechanics.
Edit: I guess you nixed that sort of thing here:
Sorry for the moot post. A shame thought. Variety = Fun (usually)