I don’t want to get too off topic here, but here’s my reasoning.
Problem #1: None of the characters are written like themselves. But that’s not really the problem. They also aren’t written consistently within the seven issues. Superman flips and flops between inspiring Man of Steel to grumpy, grizzled veteran from page to page. Sometimes the Green Arrow we know and love shines through. Other times he reads as entirely unlike himself.
Problem #2: The pacing is sloppy. Like, really really sloppy. The story crawls at a snail’s pace for the first five issues, and then seems to realize that it only has one more issue to go somewhere in the middle of issue six, which leads to every important story development occurring in the space of one-and-a-half issues. This is a good lead-in to the third problem.
Problem #3: The mystery is nonsensical and poorly constructed. Every single “clue” that the readers are given in the first five issues ends up not mattering at all. The Dr. Light stuff? Red herring. The Deathstroke stuff? Window dressing. The Captain Boomerang stuff? Emotionally hollow fluff. It never comes back. Every actual clue comes in the last two issues. The footprints on the brain come in the sixth issue. Jean Loring’s confession comes in the seventh issue. The only actually important stuff happens in #1, #6, and #7. And, honestly? A three issue, tightly-plotted murder mystery with the Justice League sounds kind of cool. Shame that isn’t what we got.
Problem #4: Jean Loring’s guilt makes no sense and borders on sexism. The woman’s motivation for murder is that she broke up with her husband, but she “needs a man” or something. It reads like “b***hes be crazy” made into a plot point. Plus, why did she bring the Atom suit and the flamethrower to see Sue? “Just in case?” Just in case of WHAT? Not to mention, the Atom suit doesn’t shrink items down with it. It isn’t the Ant-Man outfit. None of it makes any sense.
Problem #5: Making the Silver Age dark. People like to complain about the sexual assault and lobotomies, but really the presence of those things as plot points isn’t what bothers me about them. What bothers me about them is that they’re handled with all the grace and thoughtfulness of Die Hard with a Vengeance. Sue Dibny’s emotions are never explored to any greater depth than “she’s sad.” The whole thing is viewed as the Justice League’s tragedy, not hers. Not to mention, it has no reason to be there. It never ends up becoming important, it’s just a red herring in the book for shock value. As for the lobotomies of Batman and Dr. Light, it just rings as remarkably unsuperheroic, and it makes those old Silver Age JL comics really hard to go back to. They all really hated each other. They all cared way more about their secrets than doing the right thing. It just doesn’t work. Also, again, none of that ever comes back. It all just goes away once the tiny footprints pop up during the autopsy.
Identity Crisis is just a bad comic. No bones about it.