More things towards Allied warfare, like being able to easily give units into a AI players control, AI players fighters protecting your citys that are in range, and an increased bonus to both side for trade. These are just a few example, but it could make wars of huge alliances better.
Another idea I had is for citys you liberate(ones that used to belong to one of your allies), they will switch over to the AI players control after 1-5 turns(depending apon distance from capitol maybe). Also have it the same for citys AI players capturing your citys when they're allies. It makes no sense to lose one of your citys, have an allie capture it, and then watch him keep it.
Just think of the uproar that would have happened if America and Britain kept all of France.
Of course, you could include an option to not surrender it, and break the alliance. Anyway, tell me what you think and post any other ideas on this sort of thing.