Well, that was pretty articulate and full of great ideas! I've never seen someone who could write so well while drunk.
I think that the storyline you mentioned would best be fit as a prequel to AI War (anywhere from 800 years and a few weeks before the events of the normal game), and, well, it sounds perfect.
The "civil war" mentioned in-game doesn't necessarily mean only two factions, there could have been two large superpowers and a scattering of small states throughout. It would make sense that those two superpowers would have been the ones to develop the AI technologies that are the cause of the events of AI War. I guess it could be tied into the normal gameplay formula by having you play as an underdog of a number of factions, with significantly less forces compared to the two "superpowers". In this way, it could be pretty much the same, as the two AIs are too busy dealing with each other to focus on you too much, sending occasional waves, etc.
The boundaries of the factions would fluctuate over time, and with diplomacy, and conquest, your faction would rise to the strength of the superpowers, at which point, the AIs turn and curbstomp everyone.
This could even be tied into the normal game by having it transition smoothly into AI War, allowing you to keep research, ships, etc. at the cost of a higher AIP.
Yeah, I guess that would be a nice expansion to add. I can see multiplayer as a form of competitive mode here - with multiple small states each under the control of a player.