Some desired improvements, while ignoring the mission based diplomacy model. I'm guessing just about everyone doesn't like it or would at least prefer something else.
Starting at neutral instead of I hate your guts. Nothing wrong with having a cease fire with everyone at the start. When you run out of neutral stuff to play with, the AI can then just start wailing on whatever is available. The only difference would be that alliances are more likely to be formed than they are now. The AI doesn't just rush over to pummel on each other already, neutral targets are easier to take.
A civ4 style relations chart showing who is allied, who's at war, and who's sitting the fence.
I'm just guessing here, but fair diplomacy. What applies for me should apply for ai sides as well. If I have to accomplish missions to gain favor with an ai, other ai also have to do the same. It feels unfair, but without solid documentation I'm not actually sure I end up in a 6v1 after killing off the other three sides in a random huge every time.
Now, the mission system...
If they must stay, a necessary suggestion.
Fair missions. 15 minutes to take out 8 tactical structures that I have to conquer three planets in another solar system to manage is just... silly. Static reward/penalty systems when you're doing absurdly difficult tasks really bites it. It's a mini-game from hell. I seriously doubt I'll ever keep an AI in the late game on a multi-star map. It's just not possible to complete every task, and as soon as you drop to 85%, they have a nasty habit of switching to enemy and attacking your unprotected flank somewhere. With maxed out diplomacy modifiers as TEC, it's probably possible, but I really don't think it can be done in a random huge at normal settings.
Getting rid of them, now this concept I like.
Real reward/penalty systems. AI is allied with another AI? If you attack one, you piss the other one off. AI at war with another AI? Attack one, make the other one happy. Penalties for conflict, rewards for shared enemies. A trade system would be nice too. We've already got artifacts. Use them. Setting up trade with an AI should be more than just a button. The ability to share or trade artifacts, obviously a diplomacy modifier would be in order. You get a jump drive relic, share it with your neighbor, don't break the cease fire, and over time, your trade relations and peaceful status improve your relations. Coming to the defense or supporting an attack should be a nice big boost too. Taking an enemy planet should be huge. You can even do the reverse, demanding too much from your ally should stress the relationship. Setting down pings for them to respond to should cost you.
The current system is hugely shallow, even keeping it there is vast room for improvement.