I think that's a little bit of a strawman when it comes to this particular thread. I think we're being level headed about it. Comics can and should feature all kinds of stories. What makes mainstream DCU comics different from other comics is a sense of fun, adventure, and craziness that IC is a 180 from. If "Watchmen", DKR and "Killing Joke" had never been published, maybe IC would be viewed differently? But I also kind of feel its flawed on basic storytelling level: its a mystery that doesn't play fair with its own rules.
There is no one "correct" version of the JLA, and that's a big strength of DC. If Identity Crisis wasn't an "event" that lead into even worse events like "Infinite Crisis" it would just be something that I could ignore. Its just not a transcending masterwork that rises above its problems, like say "Watchmen." To me "dark" stories from DC rarely work. They have to go waaaaay over the top for me to like them, which explains my strange love of Injustice!