Why did Batman 89 having the Joker having killed the Bruce's parents cause a lot of resentment?
I don't know if it caused resentment, but it was certainly revisionist, and I didn't care for the way it forced Batman's origin to fit the stock revenge-movie formula by having Batman's motivation be to exact retribution on the murderer of his parents, rather than just to fight crime and protect the innocent, which should be motivation enough for a superhero. I preferred the way
Batman Begins made Bruce's desire for vengeance into a wrong path that he had to learn to set aside in favor of justice and protection.
Besides, having Batman be inadvertently responsible for the Joker's creation has value in giving the Joker a reason for his obsession with Batman, as well as giving Batman a sense of responsibility for stopping the Joker. But having the Joker be reciprocally responsible for Batman's creation is, as
Aragorn said, just too much a case of small-universe syndrome.
Anyway, I've never liked the idea of giving the Joker an origin at all. I wince whenever any later production uses the name "Jack Napier." At least the DCAU eventually established it as an alias (which it should be, since it's obviously a pun on "jackanapes"), but now
Batwoman is using it as the Joker's real name. I prefer it when his true identity is unknown.