I largely disagree with the OP. I don't think most of these are issues.
On being attacked while Friendly: I feel like this is the developers' attempts to make the AI more opportunistic and more like human players. In Civ V you had a lot of complaints about AI diplomacy where people thought the AI's were being too unpredictable when they were actually being more like human players.
In Civ VI, the game is heavily oriented towards war in the early game. As a result, I tend to attack whoever spawns closest to me, regardless of what civ they are and whether or not I like them. It seems like the AI is doing the same thing.
Also, the developers made it clear that they were trying to simulate different eras, especially emphasizing that Ancient/Classical warfare was a lot more common. I think they did a good job at that. In Civ VI, you do A LOT of early warfare, and get declared on a lot early on. But as you progress through the eras, war becomes less common.
So being declared on while being Friendly in the Ancient/Classical era, is A LOT different than being declared on while being Friendly in the Modern/Atomic era. So I think you are conflating two separate issues.
You also did major warmongering by taking so many Chinese cities. There are actually plenty of ways around warmongering or to keep it under control, so it doesn't look like you really understand the system.
In Civ V, there was also argument over whether civs should get angry at you if you conquer a civ they haven't met yet. However, with the rumor/diplomatic visibility system, it makes more sense that they would hear about that and be displeased, even if you don't know any of those civs. If, for example, we met an alien civilization and we learn that it previously conquered 100 other alien civilizations, none of which we knew, I think that would definitely be a cause for alarm and we would consider them warmongers.
You also point out how England is angry at you for warmongering even though it has denounced China. That is fine and consistent. In a situation with multiple poles, you *don't* want one of your enemies completely defeating and absorbing another. That would be too much of a power gain. So during the Cold War, while the U.S. might want Russia and China to be fighting each other, they *don't* want one to completely win and absorb the other - that would be a major threat.
You seem to reference Civ IV a lot. I liked Civ IV, but it had plenty of issues as well. One annoying thing was how each civ had another civ they hated the most, and if you traded with that one civ, you'd get a diplomatic penalty. But it was hard keeping track of which civ they hated the most at the current moment. And while I liked the attempt at Permanent Alliances, it got messy when diplomatic penalties were applied (since the other AI's might hate your new alliance partner).
I think the current relationship system works just fine. I don't agree with your comments that "it isn't working" or with your need for real-time information and instant gratification. The modifiers simply show a snapshot of what is affecting things but it builds up over time so the Relationship tracks things over time.
Mathematically, it's like the relationship is the integral over time, while the modifiers are the derivative which show the current direction and magnitude of change.
If anything that is more realistic since relationships need to be built up over time, rather than doing a complete 180 because of something that just happened. In Civ VI, I feel like I have to work more towards building a relationship than in Civ V. (Though there aren't as many clear benefits at the moment).
If you look at actual geopolitics (and human relationships), centuries of enmity and conflict aren't so easily overcome.
In your case, this all goes back to your MAJOR warmongering which took place over centuries. That was negatively impacting your relationship over time. Think about the -100 warmonger penalty building up over 100 turns. That is a lot.
You claim that people don't care about what happened centuries or a thousand years ago. I disagree.
The U.S. and Australia still get flak about their warmongering against native tribes and that was centuries ago.
There are some in Mexico who still want the territory that the U.S. took 150 years ago.
The U.K. still gets accused of its imperialistic past which was centuries ago.
Argentina still wants the Falkland Islands from the U.K., even though this issue is centuries old (and it was unclaimed at the time).
Germany and Japan still get reminded of their WW2 warmongering which was 70 years ago.
Israel took (or reclaimed) territory 60-70 years ago. You think the Muslim world is going to let that go any time soon? What is more, a lot of countries who have never had any issue with Israel, nonetheless have denounced Israel because of their economic/diplomatic ties with Muslim countries. Sort of like how Gandhi/India denounced you because they are friends with China and you have Chinese cities.
As a passionate Byzantinist, I still have grudges against Venice and Turkey over the Fourth Crusade (800 years ago) and over Turkish-occupied Anatolia and the takeover of glorious Constantinople (600 years ago).
There are lots of nationalistic irredentist groups who want to reform Greater X, consisting of past territories that the people used to control. This is the perfect example of those who still care about things that happened centuries (or millennia) ago.
In Islam, there is the concept of Dar al-Islam. On the extreme side, some consider any territory that used to be Islamic to fall under this category, including Spain (when it was Al-Andalus 500+ years ago).