Lots and lots of good points here.I particularly like the ideas put forward by Seasoned Alcoholic from Civ2.I would however add something else to the whole diplomacy section of the game.I believe we should have a scale or a rating with each faction even if it was something simplistic like the progress bar in MTW to show your standing in the GA mode.For instance if you formed a trade agreement with a faction you might move up the scale to 1 with that faction.If you married one of your Princes to the youngest Princess of a rival faction you might move up the scale with THAT faction to 2.If you married one of your Princess's to the heir of another faction thus making her the future Queen then you should move up to 4 (just as an example,i'm still making this up) on the scale.Also this might unlock further Diplomacy Options that might have been greyed out on the options list earlier.When the heir becomes King and your beloved daughter becomes Queen you would then have even FURTHER options in your dealings with that faction e.g most favoured trading nation, guarantees of military assistance in the case of an attack by an outsider not allied to that faction.If you attacked someone without first declaring war or maybe even without letting your ally know about it maybe you would move back down the scale with that faction and even with some other factions you are not even dealing with yet (a negetive scale ranking).
I think religious agents should also have some diplomacy and conversion options e.g dropping an Iman on to a Catholic General might reduce that mans faith(or strengthen his resolve in case of failure) or even start to convert him if his faith is low enough.What if this could be done to Kings or Heirs e.g conversion of state religion could become a possibility and maybe opening up the tech tree for new buildings.Maybe even the formation of a secular state with freedom of religion (imagine the loyalty issues arising from these examples).

Okay i'm done.Just a few ideas i threw out there.Good?Bad?Probably too hard to implement.