Don't know if this was suggested, since 145 pages is a lot to go through, and while I like to imagine that Steve eagerly watches all the stuff I throw onto Youtube, I know he's probably too busy to, so I'd like to suggest an eventual expansion on diplomacy I like to call: Local Wars vs. Total Wars.
Scenario for your consideration: You have an alliance with a neighboring empire. You have three JPs leading to their systems where you are neighbors. Neither empire claims the other's systems, so there is no border conflict, just a border. You still lay mines and defensive platforms/patrol fleets at the JPs because good practices (as does the NPR), but you never expect to use them because hey, it's a comfortable peace - they're just there to keep the other guy honest.
Now, in some distant (but not TOO distant) system, you run into some really rich deposits, but your neighbor has some ships who have just shown up there as well. You each have a few light combat vessels there, but neither side is willing to concede this resource deposit (both empires claim system, neither concedes).
Now, in the current system, there are three outcomes:
1) Diplo teams manage to keep the diplo score above -100 long enough for someone to drop a colony in the system, and the AI bails out.
2) The refusals from either side to vacate, or the empires fail to yield even after colonies are set up, and leads to a reduction in diplo score until one empire declares war at -100.
3) You think you have an advantage and decide to "give them a nudge" in that system by firing a shot at their (shielded) ships to kindly ask them to "no really, go away".
the first instance is already fine, but in either of the latter instances, diplo score ends up at -100, which leads to war.
What happens then? A battle breaks out in the new system, someone wins, well done. This is fine, and is meant to happen.
But what happens at the rest of the border? Mines arm, and go after merchant traffic. Your own ships now consider the hefty trade ships in your systems valid targets, as do their ships to your merchants in their systems. Mass murder all-round everywhere, diplo score plummets to -bazillion, you're now in a total war with your once ally. Even if you don't attack them, you still have to send your diplo ships into their systems to try and bring your score up, and if they get shot at on transit, or trip up on mines, that just makes things worse. And how long is it going to take to claw back ALL the diplo points to get above -100? Especially if they send through attacks from their systems? Do we agree that this is a problem?
To give a real-world analogue, it would be like a new island full of oil appears in the middle of the Atlantic, the US and Russia both send a pair of destroyers over, one of them fires a shot that does minimal/no damage, and both countries decide "welp, time to launch all the nukes, lol!". It just doesn't make any sense!
So, I have two proposals:
1) The quick-fix: Make ship damage ONLY decrease diplo score while it is above -100. This way, your diplomats can try and work towards peace, even if you're still fighting off raids from the enemy. This lets you work towards peace as long as nobody invades anyone's colonies. It would also largely remove the necessity of a "warscore", as the value of the rep below that war threshold, plus ongoing combat and invasions, plus diplo team efforts and skills can somewhat account for that. But while easy to implement, it's so un-satisfying, and will still spike mass-slaughter among merchant shipping while the score is still below that threshold of war.
2) The better solution: Expand into a two-tier diplo system.
The way it would work is like this. Each empire has two ratings - one "global" relations rating, and one "local" relations rating within each system where there is a known presence. When combat and damage happens, that local system's diplo rep plummets and you can go about your shooting and killing in there. While there is no combat, the rep climbs back towards zero (where it stops contributing to global rep) or, if colonies are present, towards a baseline set by the global rep level. Diplo teams that can work on that empire can target that system to raise the local rep in that system (rather than just raising the "global" rep overall) and can do this from within any other system (so they don't have to work in a warzone).
The "Global" diplo rep is determined by the average diplo ratings of every system's local score.
Local rep would initially start at the global rep level (upon discovery of the presence of the other empire, so as to not alter the global rep), and tends towards whatever the current global rep is as long as presence continues to be detected. If no presence is detected after X months, or no colonies are identified in that system, then the system is eventually removed from influencing global rep.
So in the above scenario, you would have 6 systems with +1000 rep (one each either side of the JP border), and one system with -1000 rep where your fleets are having the fight over the new territory. Fleets within that system would be at war, and will fire on one another as they desire, but the "Global" diplo rating would be at like +700 points ((6000 - 1000)/7). This means that, as long as you don't engage any ships anywhere else, trade will continue to flow, and the border will remain cordial (with perhaps some minor tension).
However, if you let that conflict fester, then the local rep at each of those other systems will start trending towards the new baseline of +700 instead of +1000, which will start dragging the global score down [((6x700-1000)7)=450], which will drag the local scores down, leading into a loop that eventually brings the global score to -100, at which point total war breaks out. This way, you can't have a perpetual border conflict without any diplomatic penalties, but a single border conflict doesn't instantly get you there, and you have time for diplo teams to bring the local score for that system up if you avoid confict in that area.
The AI would also be aware of this, and would re-evaluate whether it wants to give up on that system and let diplo teams pach up relations, or whether that system is valuable enough to eventually escalate into total war.
Having a hidden third value "Desired Diplo Rep" would accomplish this by letting NPRs decide at what point are they willing to let relations fall to. For example, a low-militancy empire that is gaining a lot of wealth from trade, espeically to the point where it would go into debt without it, might not be willing to fall below the threshold where that trade is cut off, and would pull back from contested systems if the rep falls low enough to threaten a trade treaty. A highly militaristic and xenophobic empire that doesn't benefit economically from your own very much, with a much stronger military, would be much more willing to let global rep fall into total war.
I think that something like this system would give a lot more flexibility and depth to diplomacy and allow things like border conflicts to happen without plunging both empires into total war the second anyone fires a shot at anyone else. It doesn't make sense that two long-time allies would instantly go into total war over some minor damage (and not even destruction) to a corvette in some distant system far from the core worlds.
I also understand that this would mean a lot of work on diplomacy and would not expect to see this in the current release, and I fully expect Steve to be burnt out on diplomacy and be much more keen to work on literally anything else, but perhaps later on down the road something like this would be really awesome to see.