The way I envisioned it was like this. Player A hosts a game with 5 open slots, and let's say he immediately invites players B and C into the game and makes the other two slots AI controlled. During the course of the game, player C has to leave early (work, sleep, house on fire, etc.) so he exits and now it's just players A & B duking it out, with player C's faction taken over by the AI. Now players A & B wants to invite a buddy, so they call up player D, he joins in and sees three open factions and joins one (There is an option for the host to either allow the joining players to choose or host chooses for them). Could be player C's faction, or any of the other two that were AI controlled from the start. So player A, B, and D are duking it out, player E comes in and joins, but only stays for a little while and then leaves. And then comes 4 AM in the morning, all the players get tired and log off, with the game automatically saving the state of the universe for each player. Note, however that player C has a "young" version of the universe, so if he hosts that game, and players A and B join his game, they will be, in essence, going back to the time where C left. Now if A, B, or D hosts the game, and C joins, C will have have the updated universe (along with the old version perhaps), and be able to join any of the open factions.

This is how I envisioned having multiplayer work. This would allow for a more dynamic universe, and allow for greater story telling. I hope all this made sense. Let me know what you think!