I have downloaded 2.02 now, and the Problem has shifted. The AI is now incapable of winning wars in the super late game. Since 2.02 is save game compatible, I continued my playthrough and started a second war with this Federation. War exhaustion took far longer to rise, which initially pleased me, and thus I was able to fight a war of attrition with them. But eventually, I reached 100% of course.
What happened then was not worse, but somewhat baffling to me. I'm playing a militaristic democracy with utopian living standards for everyone and the Harmony tree completed. I never even noticed the -20 (%) happines. The war continued for another 25 years after I hit 100% exhaustion, and since I had 1000 unity stored before that point and already had all of my desired traditions, I had little incentive to stop the war before taking 50% of the territory of the Federation and then calling it a day because I was getting tired.
The new system may be highly functional in the early game, but it renders war echaustion inconsequential in the late game. Especially for democracies, the form of government which should suffer from war exhaustion the most. The new system allows me to fight wars according to my capabilities, but it might aswell not exist due to how inconsequential it can get.
My Idea towards how the penalties should work is the following:
1. Instead of a flat -20 (%) in happines, one should get a -10 (%) each year for the first Ten years, -20 (%) each year for the subsequent decade etc. Thus, one would hit -300 (%) happines after 20 years. It's going to change very little in the early and midgame, but it will keep the system relevant in the very late game, because no amount of utopian living standards or chemical bliss will save you from a population which is basically running Amok at some point.
This change will however allow wars to last longer the bigger and the more advanced and Wealthy your empire is, which is a good thing in my book.
2. Instead of making influence gain a flat zero, the pacifist faction should start existing as soon as you hit 100% war exhaustionif it isn't around already, and gain 20-100% ethics Attraction each year. Additionaly, it should get a negative happines modifier for each peace offer you reject. Thus, you will essentially be confronted with an ever-growing angry Mob of pacifists while all of your other factions are slowly but surely being rendered insignificant. This will cause you to lose your influence from factions pretty quickly. Especially if the pacifists get a dice roll each year which allows them to infect another faction with a "pacifist influence" modifier, which makes them angry aswell. This last part of course shouldn't work with militarists and Nazis, but they should still lose pops to the pacifists.
Furthermore, factions should be able to enforce their Ideology on the state if they hit 75-85% Pop support and their faction leader is currently the ruler. That's of course so that democracies and oligarchies -within which the pacifists will start to win elections- are less able to fight prolonged wars than dictatorships and empires. Because that's just more authentic. And if you have pacifists in power at this stage of the war, well... what about the forced status quo making a return in this specific situation, because the pacifists have taken control.
3. I know that this is a little stupid, but since unity is generated not by how conformist or happy your pops are with your current Ideology but by buildings, pacifist pops which sit in unity producing buildings should refuse to work, thus gradually reducing unity.
4. This is more of a Personals thing than a real suggestion: Give admirals and generals the ability to rebell with their navies/Armies fight you and stage a coup d'etat if one of the following falls true:
-your population has over 75-85% pacifist support, is not a democracy/oligarchy and said admiral/general belongs to the pacifists.
-your population has over 75-85% percent pacifist support, has elected the leader of the pacifist faction as ruler (and thus is a democracy/oligarchy), or is ruled by a pacifist for some reason which now enforcer pacifist ideologies, and said general/Admiral is part of the militarist/nationalist faction.
The coup d'etat should be successful if your Capital planet is conquered by the rebels, and they should enforce their ethics and Ideology. And to add a little something to this, you should be able to choose if you want to lead the loyalists or the rebels in this civil war. Just like in HOI IV or total war empire.