This is obviously something I don't expect tomorrow, but it'd be great. you could be allies, or if you are enemies, you fight over systems. if one attacks another, and loses, he loses the war, but if he attacks and wins, he gains the system (as he did not attack the main com, unless it as stationed on that tile, and therefore killed a henchman) fight to get as much tech as possible, and if you lose a system, you lose the associated tech and your enemy gains it (even if it is a data bank.) Once you are confident you can beat your enemy faction leader (as it will be a multiple planet system and will have several automatic AI allies) you can take them out and win the war. EDIT: This just occured to me, but it would be a turn based game. The important thing to remember is losing an attack loses you the war.
I don't think losing an attack would lose the war in this version. Remember, the single player and multi player versions will be vastly different. Most of us really hope tech won't be a variable on this mode. Anyway, it'd probably be a galaxy, you claim systems, enemy has systems. You attack, win, you gain a system. Now it's their move, they either claim neutral territory or attack your system, and etc... Think of it like Galactic Conquest on battlefield. (I'd kinda like little boosts when owning certain sytems.)
How about a simpler version , instead of being actually multiplayer, since PA is online-only, when galaxy is generated, it will take some of the commanders from current players for some of the planets. By "taking commanders" I mean faction, model, name and current tech they have. So, basically AI with looks, name and tech from actual player. To avoid confusion, nickname might be modified as, say "EF32's Auto-Commander" or something like that. Or, actually, not use nickname at all, so we won't get DickLords's Auto-Commanders. And wait, here's the sweet part. You can even send notification to person who's AI replica was beaten, and proposal to play exact same same match with exact same settings, except you will control your commander now, and one that was human before will be AI now.
Solution is simple, if you are not online, you won't get 'real' commanders. You'd only need connection for the time you start new GW, and if you don't have connections, well everything will be as it is now for you.