Superwoman is Owlman's sadistic lover, a self-proclaimed "psychopathic murderer" who gets off on hurting others on both personal and grander scales. Reigning alongside fellow Syndicate members in threatening the entire population of their Earth, Superwoman is eager to aid Owlman in his plot to annihilate all worlds across the multiverse, actually aroused at the idea of ending all life across all realities while betraying the rest of their allies. When confronted by Batman, Superwoman goes about beating him brutally and torturing him, threatening him with the fate of either dying at her hand, or becoming her personal "pet" to do whatever she wants with.
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, nor even sharing the same Timm-inspired art style. 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.
Fan-Preferred Cut Content: This film was originally going to be in continuity with the DCAU and would have bridged the gap between Justice League and Justice League Unlimited. For many fans, even those who enjoy this movie, it was a shame that this never happened.
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, 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 was a lot of potential to be had to watch 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 the interaction between Batman and Jester.
There aren't really any meaningful interactions between the Justice League and their evil counterparts beyond Owlman and Batman, which is a shame when you think of the possible dialogue that could've been as each camp struggle to understand the other's philosophies.