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.
Lex Luthor is Superman's Arch-Enemy and the current de facto ruler of the United States. Seizing control of the country after installing a hologram to assume the role of the president, Luthor proceeded to turn the entire country into a police state. Recruiting the help of Brainiac, Luthor kept the superheroes of Earth in line by threatening to kill their loved ones. The heroes that Luthor did not find useful were either imprisoned or subjected to horrific genetic experiments. After a series of raids by led by Batman reinvigorates the public's interest in superheroes, Luthor snaps and begins cracking down on any super-heroic activities. Luthor launches a missile strike against Costa Rica that kills Hawkman and Hawkgirl, while he orders his forces to open fire on a concert held by "The Superchix". Luthor has Brainiac kill thousands of people in Metropolis in an attempt to discredit superheroes, not caring at all about the innocent lives lost. Luthor later captures Batman and begins torturing him while gloating how the rebellion has given him the perfect opportunity to use his satellite defense network to kill most of the world's population and allow him to rule what's left. Lacking any pretenses of helping his fellow man, Lex Luthor is motivated entirely by his lust for power.
Brainiac is an alien cyborg who partners up with Lex Luthor in order to make sure that Superman is compliant with Luthor's regime. Holding the bottled city of Kandor hostage, Brainiac murders a Kryptonian family for every time that Superman refuses to follow their orders. In an attempt to publicly discredit superheroes, Brainiac attacks Metropolis and orders Superman to not fight back or he'll have all of Kandor destroyed. Brainiac proceeds to wail on Superman when he refuses to flee, and continues on his rampage. While he is eventually stopped by Superman's daughter Lara, Brainiac's assault ends up killing thousands of people, including Captain Marvel, Jimmy Olson, and Lois Lane. Lara travels to Brainiac's hideout to free the citizens of Kandor by pretending to surrender, but not before Brainiac attempts to turn her into his subservient slave. Driven by sadism rather than his usual logic, Brainiac takes immense pleasure in the pain and suffering that he causes others.
Designated Hero: Batman, who displays very little regard for human life, despite his aim at overthrowing Luthor. He breaks into Luthor's office early on and has the chance to end things right there, but 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 his 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.
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.
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).
They Wasted a Perfectly Good Plot: A story about a dystopic future where an older Batman has to team-up with several other older superheroes to take down Lex Luthor and Brainiac is a fantastic idea. Just not when it's buried under tons of bad art, talking heads, internal monologues, hamfisted social commentary, poor characterization, and dumb subplots about a new Joker.
Uncanny Valley: FM was pretty new at using Photoshop and this was his first attempt to make a full book with it, and it shows.