Fanfic Fuel: Who else was part of good!Lex's Justice League? What was their story?
Fanon:There are people who place this in the DCAU despite the film not officially being part of it. Of course, most of the developments in the film still fit in that continuity very well, which makes more sense with most of the story intact from the unmade version.
Nightmare Fuel: Owlman being an Evil Counterpart of Batman voiced in a Creepy Monotone by James Woods is intimidating enough, but the fact that he wishes to destroy the fabric of reality out of sheer nihilism and almost succeeds is what solidifies him as one of the most frightening villains ever faced by the Justice League.
Romantic Plot Tumor: The main story is about the league trying to liberate an alternate earth from an evil Justice League, but a good deal of time is spent developing a romance between Rose Wilson-2 and Martian Manhunter. Had the story taken place in the DCAU (as originally intended), it would have probably been valuable character development for him (indeed, in the actual DCAU, J'onn is Put on a Bus to go on a soul-search to learn how to connect to humans at about where the movie would've been), but it's pointless when that's taken out of the equation.
Squick: As Superwoman is a copy of Mary Marvel rather than Wonder Woman, this implies that she's in her late teens at the oldest. Either she's good at keeping secrets, or Owlman is a creepy weirdo. Moreso, at least. Also, when she casually reaches over and snaps one of Batman's ribs like she was breaking a twig, while outright stating that she gets a sexual thrill from it and likes to do it to all her lovers.
Strangled by the Red String: Rose Wilson has a crush on Martian Manhunter. The Martian inadvertently discovers they're "attuned" when he accidentally reads her thoughts (something he'd never do by accident with a non-attuned person). He then Mind Melds with her so that they can get to know each other instantly and fall completely in love.
There's a lot of potential to be had watching from Superman interact with a noble, heroic version of Lex Luthor. But, aside from beating up Ultraman once, the alternate Lex more-or-less fades from the plot after bringing the heroes over, and he and Superman barely share two scenes.
It would have been just as interesting to see interaction between Batman and Jester.