These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Actor Allusion: In a one-panel cameo, The Joker looks just like Jack Nicholson in the Tim Burton Batman movie. This is a general rule for all Alex Ross publications that feature The Joker. Likewise, Alex Ross clearly looked up what Frank Gorshin looked like as an old man in order to draw The Riddler.
Anvilicious: The series is not exactly subtle in its themes, metaphors and particularly religious symbolism.
Magog ended up becoming this for the writers; they initially made him a cliched representation of everything they hated about Nineties Anti-Hero and the culture he represented, but he gained unexpected depth through the writing of the series until he ended up being one of their favourite characters from it.
Nightstar due to being a walking representation of the marriage between fan-favorite coupling Nightwing and Starfire.
Kid Flash is also quite popular and has made frequent appearances in the regular DC Universe long before Superman did.
Seeing Ted Kord alive and well in this book stings pretty hard considering his treatment in the main continuity.
Likewise, knowing Lian Harper is alive and a hero like her father considering the events of Justice League: Cry for Justice. It becomes even harsher in the novelisation, where the entire Arrow family are killed off by the nuke.
At one point, one of the "newbloods" calls out Superman to argue against the notion that they have saved lives thanks to their willingness to kill the most dangerous supervillains. While the new "heroes" are clearly reprehensible and vile, the reader is almost certain to find themselves agreeing there are some criminals who should be taken down permanently, rather than being given relatively light sentences.
And they also note that the traditional heroes never had to deal with threats like Genosyde and the Murder Squad - if they had a better answer for those situations, the anti-heroes are all ears.
Though it's also said earlier that Genosyde blew up Belle Reve penitentiary, Arkham Asylum, *and* Blackgate killing most of Batman's enemies; this seems to imply that Genosyde was simply a more extreme version of the killer vigilantes we see in the main series.
When Superman questions Wonder Woman about bringing a lethal weapon (a sword crafted by a deity) to quell a riot, she shoots back that not everyone has built-in deadly powers like heat vision or bullet-proof skin.
Considering that the Joker is an unrepentant mass-murderer that both the system and the 'classic' superheroes haven't dealt with yet, is it any surprise that the Magog's killing him is supported?
Woobie: Captain Marvel; a scared little orphan boy suffering from PTSD only to be taken advantage of in his vulnerability by Lex Luthor, enslaved into adulthood by bugs inside his brain only to die for the future of his people when he gains his freedom.