Expanded Diplomacy. I don't mean like Diplomacy 3.1. I mean like Diplomacy XP (SP2). No more "he loves me, he loves me not" relations. Diplomacy isn't puppy love. I'd like to see at least three scales: Like Me, Fear Me, Trust Me. The first is affected by stuff like having the same or different Ethics, having multiple Trade routes, and lending assistance in war. The second is affected by Military and Economic strength, allies, and geographical proximity. The third is affected by Ethical alignment (not the same way as Like Me; after all, two Evil civs can like each other, but they definitely won't trust each other), previous Diplomatic actions, and following laws or previous agreements / breaking treaties / declaring war without warning.
Trading for non-military Techs would be affected primarily by Like Me. Trading for military techs would be affected primarily by Fear Me. Asking them to take Diplomatic actions (declare war, sue for peace, enact an embargo, buy/sell IP) would be affected primarily by Trust Me.
There should be two types of Diplomacy: open Diplomacy (other civs know about it), and closed door Diplomacy (other civs MIGHT find out about it with Espionage, and they MIGHT tell other civs in turn). Closed Door Diplomacy affects Trust Me (and of course requires a certain amount of Trust Me from your partner). Also, Espionage determines if you find out about closed door Diplomacy between AI's. If you find out that A asked B to declare war on C, and you go tell C, your Trust Me score with C determines how much C's relationship with A is affected. Your Like Me score with A determines how much your Trust Me score with A tanks. For example.
UP laws should be breakable, but with serious diplomatic repercussions. Trade embargoes, loss of a UP vote in one session, and other UP laws that are passed that only affect the offender.
Treading in other civ's Area of Influence should not be done lightly. If the AI notices, they should react appropriately - depending on whether they like/trust/fear you, whether your flagship passed through the outskirts of their civ or you parked several fleets next to a planet, etc... Building an Influence Starbase in their AoI should be a serious no-no.
Shooting at each other once or twice should not result in immediate war. For ex: Taking out one of their starbases in your own AoI should make them mad, but not be a call to arms.
In addition to the regularly scheduled UP session, each civ should be allowed to propose UP sessions once every six months (max. twice a year, and a total of two impromptu UP sessions a year). Requires a vote by all UP members, but not controlled by Influence - each civ gets one vote. In addition, the proposer gets to pick a would-be law from a short list. Should be able to buy / trade for a civ's vote on whether or not to convene (possibly even their yea/nay vote on the actual law, but for a Very Steep Price). Trust Me comes into play, here. If another civ doesn't Trust you, for example, it might be unwilling to convene the UP at your request, even if it likes the proposed law. Also, the more recent the last UP session, the less likely the other civs will want to do it again. And if a UP proposal fails in session, you should't be allowed to propose it again - but another civ can, later. So it's a balance between waiting for enough time to elapse since the last UP session, but getting it in before another civ proposes one, and picking the right time to get your law passed.
AI civs should be able to do all these things, too, of course.
AI's in wars might ask you to intervene and attack their enemy, or they might ask you to intervene and broker a peace if your Diplomacy is higher than theirs or your Relations (Like, Trust) to both sides are high. You could also ask another civ to intervene and broker a peace for you! When brokering a peace, you temporarily see the assets of the AI as your own (so you put the deal together), but your relations to that AI will be affected by how much they like the deal. When having another AI broker peace for you, you still get to put the deal together, but you use the broker's Diplomacy scores and relations. But remember you had to give something to the broker, too, to get them to do this in the first place.
Lots more ideas in the same vein, but you see where I'm going with this when I say Expanded Diplomacy. Basically, I want to see a ton more options in Diplomacy, but I want everything you do (inside and outside Diplomacy) to affect what you can and can't accomplish with Diplomacy. I want it to be REALLY HARD to form alliances, start wars between AI's, sue for peace, etc... But in exchange give a ton more options for taking smaller actions to manipulate the other civs in more subtle ways.