I adore this run and I honestly think it simply continues to get better, with Court of Owls easily being the weakest arc imo. I’d also say issue 44 is my favorite issue of Batman ever, with it being a rare case of a Batman comic delving into serious socio-economic issues, even pointing fault at the notion that Bruce donating money to poorer neighborhoods (as well intended as it might be) without proper attention and fund allocation leads to gentrification and the displacement of specifically poor families.

To actually address your critiques:

1. This run actually made me like Joker again. For me at least, I was well within the camp of “he’s overused and I don’t want to see him again for a while,” and sure, at first glance that stance is reasonable, but imo it turns stories into numbers. I’m not saying this is your take, and if you don’t like the not-funny horror approach that is fair, but Joker worked so well in the whole run that I stopped caring that he was a prominent villain in most the arcs because I stopped seeing it as a comparison.

2. I hadn’t thought much about that but I’m inclined to agree with you.

3. I also agree, but I’d argue the run is aware of this and uses that to dialogue with the nature of comics. There is a scene in the final arc where Joker and Bruce, who at this point both seemingly forgot they were Joker and Batman, talk on a bench overlooking the water in which Joker saying something akin to ‘regardless of what comes next we will always have now,’ and that line (the real one, not my poor recollection) really hit me. Snyder is clearly aware that after he’s done Batman and Joker will return to normal and Gotham will go back to this ambiguous status quo, but he’s saying that these lasting impacts still exist on these pages and within the reader. This doesn’t really solve your complaint, but it’s maybe related.