If Clark wanted to, he could use his superspeed and squish me into the cement. But I know how he thinks. Even more than the Kryptonite, he's got one big weakness. Deep down, Clark's essentially a good person...and deep down, I'm not.
Captain Obvious Reveal: Hushs true identity, given the fairly transparent foreshadowing. Led to some backlash decrying the lack of a compelling mystery. Allegedly, though, it wasn't planned this way; Hush originally was supposed to be a resurrected Jason Todd, and Thomas Elliot a Red Herring, but executives got cold feet at the last minute and vetoed this.
Ho Yay: Poison Ivy's pheromones working on Catwoman is a plot point. Ivy even says that no man or woman can resist her. It helps that Catwoman is revealed to be bisexual a few years later in the New 52.
They Wasted a Perfectly Good Plot: Detractors of the story generally agree that it would have made more sense for Hush to be Jason Todd, as rumor has it was the original plan. These fans sort of got their wish, though, in the Red Hood storyline.
Crowning Moment of Funny: Bruce is on his way to a date with Selina Kyle, resulting in snark from Dick about how she likes both Batman and Bruce despite not knowing they're the same person. The next scene after that Bruce gets a video call from Damian, who starts lecturing him on dating a criminal, and insists that Bruce use protection and criticizes Bruce's driving skills, resulting in Bruce hanging up on him.
Fridge Brilliance: Nygma says that the Lazarus Pit gave him a "clarity" allowing him to learn the Batman's identity. The Pit gives sane people temporary madness, so it can have the opposite effect on someone who's already insane. As such, the Pit temporarily rid Edward of his compulsive Complexity Addiction, which was the main thing keeping his brilliant mind from finding out.
Les Yay: Poison Ivy uses a kiss to bring Catwoman under her spell.
They Changed It, Now It Sucks!: As with The Death of Superman before it, fans who had hoped for a completely faithful adaptation were less than thrilled by the number of changes that failed to live up to their expectations (the fact that the animation doesn't try to emulate Jim Lee's art style, Tim Drake being replaced by Damian Wayne, Barbara being Batgirl instead of Oracle). To say nothing of Hush actually being Edward Nygma and not Thomas Elliot.