Dano... you read my mind like a book!!
Well, just a couple (few)

of ideas I would like to throw into the mix:
1.) I hope that, in the final product, whatever the AI can do, I can do, and vice versa. There were times in GalCiv1 that I would be approached by a civ about another civ becoming too powerful, but when I wanted to perform the same action, there was no built-in feature to do so. Please do not do this sort of thing in GalCiv 2. Fair is fair, and the quality of the AI should be such that it does not cheat in any way, shape, or form (resources, options, etc.) or at least allow the player to set the parameters.
2.) I have yet to see this feature in use in any game with diplomacy in it: the ability to bring more than 1 party (other than myself) to the table and work out our deals. In GalCiv 1, there were occasions where I tried to get two races to stop fighting and instead focus on a third race that was more powerful than the three of us individually, and because I had do talk to each race one at a time, I rarely got them to be willing to "take the first step" in ceasing hostilities. If neither side is willing to take that "first step", there is no way hostilities will stop, and being able to present offers/bribes/threats/etc. to both (or all) sides of the conflict at the same time may be a way around this.
3.) By the same token, I could not get allied civs to "speak" to my enemy civ on my behalf, i.e. "convince them that I am worth more "still in the game" or unharmed or whatever. If I had no allies (even when having good alignment and non-enemy civs were good as well), it usually came down to whether I had enough military might to end the hostilities. If I did not, it was curtains for me....
4.) I guess, by extension of the above, I would like to be able to promote or warn against another race (possible consequence could be it affects my relations with the race I am talking about and possibly even the one(S) I am talking to, and perhaps other races I currently or could potentially interract with). In addition, when playing GalCiv 1, if I needed something from another civ but was unable to provide anything in return, the diplomacy defaulted to "hand it over even if you can whop my butt" and had no option to ask or beg. Also, I noticed that in GalCiv 1 I could not trade information (information acquired through spying, purchased/acquired from another race about a 3rd race, etc.) Also, a feature, if possible, would be to implement a system similiar to that used in Medieval: Total War (there, a spy piece placed where the faction leader was could based on calculated probabilities hint which other faction and province was likely to be invaded by this leader's faction). In GalCiv, it could be a part of the funding of spying, and the info acquired could be not just about war, but trade and peacetime polices, locations of units and planets, etc. The info could be good for only a limited time, after which it is out-of-date and useless. Of course, this would only apply to non-human-controlled opponents.
5.) I just now thought of a feature similar to the one above that could be used, even if there were human opponents, and that is some sort of "bulletin board" info request, where if you know in advance what you want, others (through the spy contact network) would offer to sell the info to you for a price.... catch is, is the info worth the price, or is it even true.... the possibilities this brings to mind.....
6.) The "Right of Passage" mentioned by Dano... perhaps slight modification to that where passage is granted only to a class or type of ship (i.e. civilian, trade, etc), ships heading to a certain destination, or must have an escort of warships from the civ whose "territory" it is.
Lastly, only because I do not know of which forum thread to put this, but a "old" game, the original Imperium Galactica, allowed for the player's civ to escort any vessel except those of an enemy empire. By doing this, I was actually able to enforce the peace once I got powerful enough, as no one wanted to attack a fleet or a planet being under protection by my ships. I think this would add a nice new dynamic to the game, and would help out with regards to trade routes that traveled to dangerous territories or in dealing with pirates. In GalCiv 1, if two empires were at war, neither side respected any trade routes established by my empire (those my freighter established, not that of the enemy civ). I would like a way to say "mess with my trade route, mess with me"... which may cause them to think twice about attacking those helpless merchant ships.
Btw, all of the above would work both ways, for the AI and the human player.
Whew! what a mouthful!

Comments anyone?