Personally, I vote Diplomacy being THE major feature of any expansion. Why?
1) Its an area most games lack features, or, lack character. GC never lacks for character, but features? Yeah a little, there is nothing special here (or in the past iterations) at the moment.
2) I know part of your vision for the game is immersion and a little bit of role-play as it were. Your not building the most interesting spreadsheet game, your building an experience. Diplomacy can play a huge part of that. (Also espionage can be part of this too)
I don't want to be too specific on suggestions, but generally, I would like to see a less than obvious system when trading. I'd like to have a conversation with the alien in front of me, and if I pick the right responses in the right order, get rewarded. Some randomization is needed, and different technologies can open up better and better responses.
For example, the Drengin speak to the Altarians, no diplomacy tech, your choices are:
"Hello dinner, how are you?" (This is your best response, its not great and still incurs a penalty with someone like the Altarians)
"Ahhh, what do the weak wish from the strong?" (The Altarians definitely don't like this, but it will give you a small chance for trade during the conversation)
In the future, with some tech you may get to say...
"Wise Altarians, what can the earnest, if aggressive Drengin do for you today?" Neutral enough greeting, and gives a higher chance for trading.
I also believe trading "stuff" and making alliances, non-aggression pacts, open borders, should be split. I don't think diplomacy should be as nakedly materialistic. An alliance can't be bought with some short term stuff, it should be bought with tech treaties, and generally, by having a good solid relationship in the past. Splitting them, also means you can have empires very willing to sell you things, but incredibly resistant to commitments, which I imagine the Iridium would be.
I also agree that we need more conflict that isn't outright war. I really think that influence and "real borders" need to both exist, seperately. Influence represents your culture offensive, while some small real border around your planets could also exist. Conflict outside of your real borders does not trigger war, but obviously has a diplomatic penalty and a chance to trigger war. This will really spice up the game play. I'm sure you can do this in other ways, but it requires "neutral" space, which the current influence system eliminates pretty quickly.
That is the simplest implementation I can think, I'm sure you can come up with a great system.
OH and I really hope I don't have to wait for an expansion to get mod-support via Steam Workshop. :()