Wonder Woman the Animated Movie is far superior. This is the type of movie fans want to see a live action version of. The story is humorous, characters are lovable and the music is epic. I went into this movie being skeptical that a WW movie could work, but by the end I had been convinced a WW story can deliver the goods. The dvd sales for this movie were originally low, but within the past year and a half it has shot up the DC animated movie sales list. If you haven't seen this movie, you may be missing out on one of the gems of the dc animated universe.
I really enjoyed both. JL War was more of a popcorn flick. Darkseid was more of a brute-which did hurt this movie. Flashpoint was dark but really well done. There are twists and the villain is compelling. My favorite dc animated movie isn't a movie per say-but the Cadmus arc in JLU is basically a movie and probably my favorite DC animated story.
I usually choose sides but I choose I love both of them. Both shows took relatively unknown characters like Blue beetle (for young justice) and Felicity (for Arrow) and make them the true heart of the show.