For the entire DCAU, my favorites were New Frontier and JL: Doom. Wonder Woman was pretty fantastic as well. Oddly enough, I have yet to watch Flashpoint, just because it was the reason we have the New 52 now, and I knew they'd never top the Knight of Vengeance mini without making it it's own movie.
For a new viewer, The New Frontier is a pretty good animated movie. But if you're a fan of the original Darwyn Cooke book, then I'm afraid it's a pretty big letdown.
The problem is that there is just so much to love about The New Frontier, and it should've all been kept in. This was basically the exact opposite of the problem with Superman/Batman Apocalypse, in that they cut stuff out to make a 75 minute film. They did not fit in everything from the comic, and this hurts it if you've read and loved the comic. The original source just looks so much better, and you find the omissions lacking. There are so many changes that it's hard to count, and I won't even attempt it. But the entire Challengers of the Unknown element from the story is excised, they're not anywhere in the film. And you lose a lot of the richness, that worldbuilding that made the comic so fresh and interesting and enjoyable.
Also, some of the musical choices and odd pauses during dramatic scenes felt off to me. For example, there's a big scene where Barry Allen stops Captain Cold's scheme at a banquet by tying his cold bombs to a balloon. They detonate up in the atmosphere and produce snow, which falls on the people at the banquet. Here's the actual lines of narrative in the comic:
"Then something magical happens. Cold's bombs detonate high in the evening sky."
"And for a few minutes, it's snowing in the desert. The other folks, they can't see me, but I'm there, vibrating just out of their vision."
"I'm there with them, and it's something to see."
Now, it's this rather magical and awe-inspiring sight in the comic. We're there with Barry, enjoying this light snowfall in the aftermath of a superhero struggle, and we're meant to savor the moment. It's touching and rather mellow and tranquil. The Flash is enjoying the spectacle along with everyone else.
But in the film, the same scene ends with Barry speeding off while heroic peppy music plays dramatically. It just ruins the whole tone that the comic was going for, IMO.
So yeah, these things do bother me. The overall plot with the Center does get covered, but it just feels so bare-boned and perfunctory, rather then majestic and layered. The ending with Kennedy's New Frontier speech is done fairly well, and it is poignant, but then they don't even bother animating the last scene, where the newly formed Justice League arrives to battle Starro, their first official encounter. It's just a static image, and we don't get Jimmy Olsen's excited utterance of "Miss Lane! Here they come now... it's going to be okay!" That exuberant line, denoting newfound confidence and optimism for the future, made the scene for me and to have it missing was a disappointment.
The comic is great, and the film adaptation is pretty okay because of that, but it's a shadow of what could've been.
You should get on Flashpoint, it's a damn good adaptation. The few weaknesses it has are the same weaknesses that were in the original Johns run.