At current stage all factions start on same level, anyhow they have different traits. But it's nearly all equalized.
It would be major enhancement to choose different tech-eras or expansion levels.
Tech-eras could be done in setup quite easy. Give us a drop down to choose on which era to start.
The expansion level might look similar, but needs some more into-depth programing to expand that faction on more planets.
I could even see a quite interesting option to add 'new' factions to an allready started multiplayer game. You might join in allready running games with your fresh new faction...but one has to realize that you encounter allready expanded big bullys in your neighbourship. So...are you the diplomat to sign treatys for surviving...even if it might bring you under rule of your strong neighbours? Or do you fight and never retreat? Probably you are super-researching faction...and your small amount of ships is much better advanced then your large-empire-neighbours?
All in all, I'd like to see non-balanced games, as such setup might get much more interesting.