Personally i would like the emphasis to not be on the war but rather the next phase the settling of the solar system, extra solar colonies and rebuilding. The war imo should be backdrop. Doesnt mean we cant have episodes involving the war but i really am not that intrested in a military game
If i were running it. The war would be over the sic asi that you detailed would be the ones that got away and can threaten from space. They replace the aberrants they are badily out of the picture but their threat is a constant worry. A good example is the ai war from space above and beyond.
I just dont think makjng this a war game would be a much fun