Adaptational Badass: Dawnstar gets some impressive light powers to fill out her comics powerset, which was limited to tracking and flight. And while the the Time Trapper was always a major powerhouse, he's treated like a Lovecraftian horror here, a Shout-Out to the Paul Levitz/Keith Giffen Legion run, where he was in his Entrophy Personified incarnation.
Arrogant Kung-Fu Guy: Although not your typical loner, Karate Kid certainly qualifies. It's his arrogance that causes the trouble in the first place, and it's a major character flaw he eventually learns to overcome by the end of the movie.
Enemy Mine: Averted; Karate Kid attempts to form an alliance with Captain Cold, Gorilla Grodd, and Black Manta at one point due to common interests, but the villains won't have any of it.
Evil Is One Big Happy Family: The Legion of Doom seems to have a stronger bond here than most versions. Cheetah flat-out tells Luthor that they were lost without him.
Generic Doomsday Villain: The Time Trapper's main motivation seems to be to destroy everything, without much explanation given. He's eventually revealed to be living Dark Matter, with no actual emotions beyond the desire to spread and consume.
Here We Go Again: When Dawnstar and Karate Kid return to their own time, they find a statue of Lex Luthor where the Superman one had previously stood, and so return to the past to correct this as the film ends.
Make Wrong What Once Went Right: The villains' goal is to prevent the origins of Superman through time travel. Since he inspired the majority of superheroes, this will effectively cripple the competition.
Merchandise-Driven: The film was commissioned by Target to promote its line of Justice League action figures.
Mugged for Disguise: Cheetah and Solomon Grundy rob a pair of Smallville residents for their clothes in order to fool the Kents. It's implied that they killed them.
A couple of pedestrians resemble Wendy and Marvin, walking their dog looking like Wonder Dog.
Baby Kal-El is called "Superbaby", the name he's often called in comics featuring a toddler Superman.
Near Villain Victory: Lex Luthor's plan to prevent baby Superman from being found and raised by the Kents initially succeeds. Later, Time Trapper almost kills the heroes, thereby insuring his victory, but he's done in by Dawnstar.
Nice Job Breaking It, Hero: Karate Kid kicks off the plot by showing off his ability to almost punch the weak point in the ice holding Lex. The near-miss is still enough to do the job. Later on, Dawnstar and Karate Kid try to paradox Lex out of existence, but this leads to the Time Trapper nearly destroying reality and their temporal meddling changes their relative present so that Lex is the one remembered as a hero.
Not to mention Captain Cold's bungling at the start of the film is what foils Lex's plan to enlarge the polar ice caps and seals in him in ice in the first place.
Not Helping Your Case: When trying to convince Robin that they aren't from the Legion of Doom, Karate Kid mentions the other Legion they weren't accepted into. Lacking context, this only confirms Robin's suspicions.
Sealed Evil in a Can: The Time Trapper's hourglass is both the source of his power and his can. So long as someone else holds it, he's bound to their will. In his own hands, he's free.
Plus there's the future version of Lex Luthor who's sealed in ice until Karate Kid frees him.
Sequel Hook: The movie ends with Grodd ominously claiming that with his newfound knowledge of the future, the key to vengeance against the Justice League is in his grasp. Later, when Karate Kid and Dawnstar return to the future, they find Lex Luthor has taken control of the world, and they go back in time again to fix things just before the credits roll.
Temporal Paradox: Though a very selective one. Anyone who shouldn't technically exist in the present can be erased by the Time Trapper, but the timeline doesn't change beyond that. Despite the far-reaching implications of an absent Superman, the only change seems to be that the Justice League suddenly stops existing now, as opposed to never having existed at all. This is particularly bad with Bizarro, who literally only exists because there is/was a Superman.
There Was a Door: Dawnstar and Karate Kid blast their way into the Hall of Justice, since they couldn't figure out how to get inside. Apparently the large glass doors at the front mystified them.
Villain Ball: It's noted that Dawnstar and Karate Kid have made themselves walking paradoxes, thus rendering them vulnerable to Time Trapper's erasure power. When he gets the chance, however, he just gloats that they cannot stop him (no points for guessing his undoing).
Whole Plot Reference: The story is basically a modernization of the Superfriends episode "Secret Origins of the Superfriends". The main difference is the inclusion of the Time Trapper and the Legion of Super-Heroes.
Worthless Yellow Rocks: The cab driver demands Karate Kid and Dawnstar to pay him. But they either don't seem to understand the concept of money or are unaware that currency is printed on paper.