How about a general relations penalty for maintaining a large military force.. it would seem likely that other factions would prefer more evidently peaceful rivals, and it might help to turn factions against each other close to the end?
It would have been good to have different government types. However, we could still have some of the effect- I'd also suggest that there would be an element of repugnance associated with some technologies.. Perhaps these?
Fallout, Novalith, Backroom Deals, Favoured Client, Insurgence, Foreign Sabotage
Martyrdom, Ruthlessness, Eyes of the Converted, Persuasive Offers, Inspired Wraith [sp?- Wrath]
Slavery, Shock And Awe, Expert Bounty Hunting, Raider Relations
Another separate suggestion- could it be made possible to mix locked and unlocked teams in the expansion? Then you could have human players playing locked games with unlocked AI providing possible allies, and also the abiliy to lock AI factions together as one team.