Awesome Music: The main theme (and closing credits theme) are among the best of the animated DCU films.
Complete Monster: Owlman was already a criminal and founding member of the Crime Syndicate of America. Upon discovering the existence of the multiverse, Owlman became enraged by the fact that, with every choice a person makes, they literally create another world in which they made the opposite choice. Determined that his choices had to affect not only his world, but all existence, Owlman journeyed to Earth-Prime, the Earth that supported the existence of all other Earths, planning to destroy all reality in a fit of existential angst. About as selfish as they come, Owlman was reviled even by his compatriots in the CSA.
Fanon Discontinuity: Inverted, if that makes sense; there are people who still place this in the DCAU despite the final product not being part of it. Of course, most of the developments in in the film still fit in that continuity very well, which makes more sense with most of the story intact from the unmade version.
Ho Yay: Ultraman referring to the parallel universe version of Jimmy Olsen as his "boy" might have some subtext to it, considering that unlike the comic this animated film's version of the other Jimmy is a big, strapping, hulking brute. Not a bad match for an evil Flying Brick like Ultraman, eh?
This is in part because it reminds the fanbase of the Countdown to Final Crisis series where the regular Mary Marvel turned evil, which was not well received.
It's also because if this Superwoman is Mary Marvel, that means that Owlman is in a relationship with a teenager.
Nightmare Fuel: An evil Expy Of Batman? Pretty scary. An evil Expy of Batman voiced in a cold, dead monotone by James Woods? REALLY damn scary. An evil Expy of Batman nihilistic enough to unmake reality in aformentioned fit of extistential angst? Jesus Christ...in short, Owlman is FUCKINGTERRIFYING.
One-Scene Wonder: Batman's reinforcements on the satellite, maybe the most outstanding one is Aquaman.
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 the expy of Mary Marvel rather than Wonder Woman, this implies that she is 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. Martians apparently have no need to date.
They Wasted a Perfectly Good Plot: So much story potential in watching 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.