Alternative Character Interpretation: Batman bringing up that Dick Grayson being the New Joker was the result of a long series of experiments on him by "your masters" (Luthor and Braniac). So perhaps all his taunts about having "fired" Dick, let alone his rant about it being due to Dick being a "sissy" Dirty Coward, were just to make New Joker mad so as to catch him off guard, as Bruce understood that the long-brainwashed Dick is sadly beyond saving at this point. Fridge Brilliance and Alas, Poor Villain all rolled into one.
When Dick plunges to his death as a result of the Batcave's destruction, Bruce seems to have something of a solemn or possibly saddened expression before saying "Farewell, Boy Wonder." It even looks like his eye was wet for a moment. This seems to be that he regretted his past behavior and what it drove Dick to do.
Crazy Awesome: Plastic Man fights soldiers by turning into a toilet. And then flushing them.
Designated Hero: Batman, who despite his aim at overthrowing Luthor, displays very little regard for human life. He breaks into Luthor's office early on and has the chance to end things right there, and instead just leaves. When Superman explains to his daughter why they shouldn't just take over the world, Batman actually argues against him, and perhaps the crowning Moral Event Horizon is that he assembles a rebellion composed of girls in costumes, who play no important role in the story and simply die and accomplish nothing.
Hilarious in Hindsight: The moment where, amid Hal Jordan's destruction of the orbital cannons, an Islamist terrorist calls out "JIHAD!" And someone offscreen goes "Ah, shaddap!" See: Holy Terror.
Love it or Hate it: Many dislike it for being an ugly self-parody of the original work. Some like it for exactly that reason.
Padding: There are a lot of cutaways to news programs. The second issue actually does something with them (the superheroine-cosplaying band is used by Batman to kick start a revolution), but the first issue is just top heavy with needless arguing between peripheral characters.
Shocking Swerve: Infamously, the Joker's identity as Dick Grayson comes out of nowhere and the book does very little to explain how it actually happened.
So Bad, It's Good: The art contrasts extremely with that of its predecessor in being neon, simplified, and much worse.◊ Also, Frank Miller seems to think that female pelvises are horizontally placed. In fact, there's barely one woman in the entire comic who ends up looking normal/slightly physically possible/not horribly warped, and when they do, it's usually because they're concealed behind something. Even when they are ostensibly standing up straight, they get warped into having one leg massively thicker than another or are leaning waaay over to one side.
The Atom rides a modem through the air into somebody's cell phone.
They Wasted a Perfectly Good Line Art: While Frank Miller's art wasn't exactly gorgeous, the colors were often garish, in stark contrast to the muted coloring of the original (which was done by the same colorist).
Uncanny Valley: FM was pretty new at using Photoshop and this was his first attempt to make a full book with it. It shows.