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.
YMMV: Justice League: Crisis on Two Earths
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.
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?
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), 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.
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 Just Didn't Care: Not that the movie was bad, but it can be painfully obvious that the movie was designed as Justice League Unlimited Prequel. Not much effort was put into actually retooling the story or tone outside of replacing John Stewart, the DCAU Green Lantern, with Hal Jordan - some of Hal's lines could have easily been spoken by John with no real difference.