My absolute biggest and unforgivable issue with Tim Burton's Batman was the absolute desecration of the origin story. Making The Joker, a villain that Batman can and will defeat, the man who killed his parents, absolutely takes away his character.
The whole point of his parents' murderer being a faceless thief that he can't put to justice is what drives his fight towards all crime, as opposed to this singular person he can take his revenge on. Not being able to get his revenge is what drove him to insanity and the desire to take it out on all crime.
So by having their murderer be a villain he faces and defeats in the first movie, not only does it ruin his backstory, but it takes away the actual and original motivation for being Batman. Because in the end, Batman isn't a hero, he's a selfish vigilante who was warped by his parents' murder and takes it out on "crime" by dressing up as a bat and beating them senseless.
While it wasn't an amazing movie, I feel like Super had the right take on that, by showing that he's nothing more than a violent schizophrenic beating the hell out of people for reasons ranging from absolutely necessary to completely arbitrary.
I don't mean to say I hate Tim Burton's Batman, I think Keaton has played the best Batman/Bruce Wayne so far, I love Jack Nicholson as The Joker, Prince's soundtrack is unbeatable, and the look of Gotham is perfect for the campy feel of the movies. And on the campy note, I feel like Tim Burton hit the perfect amount of camp and darkness, unlike Schumacher who tried way too hard to bring the cheesy and homoerotic tones of the Adam West-era back and failed.
So I love the movie, and I would begin to agree with the author that it could be the best, but the muddling of the origin story absolutely removes the poignancy of Batman's character.