I actually thought this was an improvement on the graphic novel

Well, to be fair, it wasn't a straight adaptation of Grant Morrison's "JLA: Earth 2." It also borrows from a 1964 Justice League of America story called "Crisis on Earth-Three." It seems to get most of the plot outline from the Morrison story, including the part where Alexander Luthor comes to "our" Earth to ask the Justice League for help. But the idea of multiple other Earths that could be destroyed if certain actions are taken comes from the 1964 story (though it's severely altered here).

In Morrison's novel, the good Luther comes to recruit the JLA, and they go to help, but find that they can't win in the other universe. Even the "good" guys are not good. Batman help's destroy Owlman's power base in Gotham, taking down Boss Gordon (in this universe a crime boss and not the police commissioner), while the anti-matter version of his father, who is still alive, is the commissioner. When Batman helps him, Commissioner Wayne turns Gotham into a police state with summary executions and martial law. An antimatter Brainiac is the villain, and the Justice League has to let the Crime Syndicate back in to defeat him, since they are good guys who can't prevail on this Earth. By contrast, the Crime Syndicate members who went to the matter Earth were swiftly beaten by Aquaman and Martian Manhunter, because they couldn't prevail on the "good" Earth.

I never liked that.

It's not just that its unsatisfying and not a happy ending, though it is -- the bad Earth remains bad, and the good version of Luthor who is trying to save it is always going to fail. It's the fact that he's doomed to fail, always, that irks me. He literally can't succeed there. And the Crime Syndicate can't succeed on the matter Earth that's home to the JLA. The same force is stated to be at work, so the good guys always win. They're destined to win. This severely undermines their heroism, and dramatically it detracts hugely from the rest of the DC Universe, since it means that, while they may encounter setbacks and occasional losses, in the end, they can't lose. Good must triumph, so it always does. It makes the heroes into beings who are no longer autonomous agents, responsible for their actions and in control of their fates, and turns them into avatars of some sort of divine fate that has preordained every outcome. That makes them less heroic, and story is more dramatic when there's a real possibility the good guys will lose, and when they do occasionally lose and have to deal with the consequences.