I'd kind of like to see a persistent universe storyline, epic hero space opera style, with one man wandering the underbelly of a divided galaxy building an army to challenge the AI for domination of the broken remains of the former Human Empire. In this version, you would control your alter ego Trader/Mercenary with a single ship in a barren post-apocalyptic RPG style universe, wandering freely from system to system, trading to make money, questing to gain faction favor and influence, and gathering information on the different factions in each system.
Each faction controls one or more systems with the AI as gatekeepers right on top of the only wormhole out of this little corner of space. The Zenith guard their wealthy systems with Border Golems that no one in their right mind would challenge... without the assistance of the Spire, long isolated over the other corner of the map. And surely the Rebel 'X' faction in system 'Y' that just developed technology 'Z' would make powerful ships provided they're paid with resources from Human Pocket Empire Number One, much to the displeasure of Human Pocket Empire Number Two through Five. I envision lots of NPC interfaction traffic; trading ships, courier ships with secrets about the AI or other Factions, criminals on the run to capture for brownie points, research vessels with technology to barter, space pirates, star ninjas, and even robot ninja pirate zombie factions! Of course the AI could care less what happens in this corner of the galaxy, so long as the fleshling plague doesn't escape quarantine to the rest of space and stays the hell away from the restricted worlds.
Missions would arise organically from the interactions between factions as you jockey for power, influence, technology and allies. Once your Human Coalition manages to acquire enough resources, technology and allies to challenge the AI Gatekeeper, you break through' into the regular AI Wars map like the Spire campaign, or 'escape' like a standard AI Wars campaign now controlling the entire resources of the local system cluster and the wormhole back to the Human Coalition Space.
I think it would be awesome to see what kind of gestalt would arise in a game like this coupling multiple factions with the AI Wars style AI decision making. Simple rules interacting in countless ways would create a supremely replayable universe. A Galaxy Without Wind.