Well first I think that alliances should carry a lot more weight so the AI actually stays allied with you for a while. If that happens, then...
You should have a "United Nations" with you ally/ies where you can initiate global trade pacts and all that, but instead of governor, you pick a representative, and that representative gets some bonuses but the real kicker would be that if you have contact with the other ally groups, you hold a grand council with all the representatives. This would be called whenever someone does an atrocity to decide what should be done, or when someone has been defeated (not conqured, just defeated, like Germany was in WWI/II, not like how Rome took over most of Europe), what should be the punishment for the civ who was defeated, and how much "compensation" goes to who and such.
Any other ideas?