After seeing all the endings (including both for each faction), they don't quite fit your victory condition you achieved (Lumeris and science victory for example). I was thinking, why not a special quest for each faction that grants them victory if completed. Now this wouldn't be game over victory, it would be more like the academy endings, in which it doesn't end the game. But instead shows the ending scene but with different dialogue (lets say the Vodyani) to everyone. The Vodyani become virtual and become a crisis to all other factions. As for the other factions, the Carvers become an unstoppable swarm, the Lumeris can corrupt other factions systems (since they have some much dust now), Horatio becomes a god, the Riftborn can terrafrom entire systems to be like their home universe, Unfallen's vines can spread on their own and even into enemy territory, United Empire becomes the eternal empire and their systems become near impossible to take, the vaulters ships can never be destroyed in battle (they survive like hero ships do), and the sophons... I can't think of something for them.