Agreed with a lot of these, with some caveats. The systems as they are not for great works/theming, chopping OP-ness, pillaging without penalty, agendas, etc... all need some hefty re-working.
But I think they are mostly cases which need some better fine-tuning, rather than scrapping. Like, for example, the great works system. If we had like 100 great artists to work with, so that everyone was recruiting multiple ones, and such that you got a big balance of all types from all eras, then the current system actually wouldn't be terrible. Like with archaeology - it's relatively random, so sure, it might take you 3 museums to find enough to fit a theme, but it's a fun little mini-game. And the fact that you can choose the civ often gives you some customization (although it's annoying that I can't go back to check my museums to be sure I don't have that pair already). But with artists, honestly I have probably themed museums once, and that was purely by accident.
Similar with agendas. I do enjoy a limited amount of personality - maybe building a large navy will be enough to appease Harald. But I agree that it gets a little too random, and it feels like too much of the game is set based on your first meeting. Too often I have a neighbour "just doesn't like me", they denounce me shortly thereafter, at which point we will feud for the next 2000 years. I definitely miss the system in civ 4 where you could see where you were, you did have times where you were "safe" from invasion, but you had to keep that up since falling behind for even a few turns could trigger the DoW checks from a neighbour. Both games are great in that there are times and moods that you know you are "safe", but both have some annoyances for sure. The current one though is probably worse, because I can declare friends, and then proceed to ruthlessly sack everything that they care about, and it's only at the end that they are shocked, shocked! that I have crossed them and may consider not renewing our friendship at that point.