In the late game diplomacy is not really a thing anymore if you are involved in the world affairs in any way other than sitting behind your walls.
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1st case: you are a warmonger, everybody distrusts/hates you and that's fair.
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2nd case: you are playing very tall, never declaring war, just rushing any non-domination victory. You can usually maintain fairly good relations with others and still have diplomatic options opened to you. The closer you get to any victory though, the more distrust is growing, that's fair.
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3rd case: you are playing wide/a mix of tall and wide and going after a non domination victory but you are/want to be engaged in world affairs. If you are attacked, you can take cities/vassalize an AI. If an AI is too menacing, you don't mind going after it. In that case I find the diplomatic game to be frustrating and unfair. The fact that you have captured some cities and/or have vassals (from the civs who attacked you repeatedly throughout the game mind you) and the fact that you get closer to a victory type makes the whole world unwilling to do any diplomacy with you (most often it's locked behind a denounciation).
I think it is a pity since it makes the late game war/diplo very clunky. You can't broker defensive pacts anymore, you can't have opened borders (since you can't have embassies for the AI is denouncing you), and if there is a domination civ in the game they can go fairly unopposed. In my most recent game I had to fend off Songhai who was crushing civs after civs. I liberated 3 French cities, 2 Chinese Cities, 2 American cities... and yet none of those AI attitude toward me changed in the least. Sometimes, without an open border you just can't project your forces at all to were they are needed. Denounciations are way too long (70 turns I think) and by the end game 70 turns of diplomatic shut down is like a death sentence for diplomacy.
I would argue that the 3rd case is the most interesting warfare wise, so it is a pity that the diplo/war system is so stiff. If you are a warmonger, by the time you reach modern/information era you are usually 100% dominant and war is totally one sided. If you are playing tall defensive, you just turtle up until you get a victory. But in the third case you usually have a strong army but the other AI, especially warmongers are a real challenge, and that's great fun. Since modern/information era is the time warfare gets the most interesting with the most potential for combined arms, it's a bit sad the game "punishes" you for wanting to participate.
The closest emulation to a "20th century world order" (other than total domination) that the game offers is vassalization. You are attacked several times, you want it it to stop, you stomp the civ and vassalize it. Problem: to do that you have to take several cities, which makes you a warmonger in the eyes of the world (even if you give back those cities right after the end of the war). On my last game I was playing tall Venice and was harassed by my neighbors. I vassalized 4 of them through the course of the game and by the end I had only kept two cities (on a huge map), all my neighbors were given back all their cities (so I gave back around 15 cities): hence, peace and freedom of commerce was ensured on our civilized continent. Here the simulation is limited: for the AI I'm sure I am a bloodthirsty warmonger (even though I never declared war myself) while I see myself as the equivalent of the US freeing Europe in 1944 and founding NATO
(and my vassals loved me, my only way of having good relations with anyone in the endgame)
I don't have an easy solution to all of this but I think a good start could be the following:
- if you liberate a city for a civ, the denunciation you might have one toward the other are lifted and you can resume diplomacy on friendlier grounds.
- liberating a city should be a bigger positive boost to relations (perhaps scaling with population of said city).
- make denunciation duration scale backward with era (70 turns in early game, 40 turns in mid game, 20 turns in late game).
- taking cities in a defensive war should be less impacting than in an offensive war (it might already be the case I don't know).
- if you vassalize a civ and give back their cities after the war, it should erase or mostly erase the negative penalties for taking those cities in the first place.