Everyone knows who Superman, Batman, and Wonder Woman are. Your assumptions are proven wrong in this feature film by Bruce Timm. In this alternate reality, Superman is the son of Zod, Batman is Kirk Langstrom aka Man-Bat, and Wonder Woman is Bekka of New Genesis.
When I saw this film, I had thought that it was a rehash of what had came before and I was very wrong. This version of Superman is more hands on than the original and will not hesitate to get his hands dirty. The story is that someone is killing the world's greatest scientists both heroes and villians from the DCU ie Mr. Freeze, The Atom, Mr. Terrific, Steel, and others. The evidence point out to the Justice League who is under scrutiny by both the public and the Government for the way how they handle things.
My only criticism is that more should have been told more about the lives of each Leaguer. I had to read the comic book one shots to get the backstory. Other than that, still a solid story. It is good to see Timm back in the DCU again after being away for a few years and was last seen working at the Marvel Universe.
It is an original story from Timm which is why the story is good. This is one of the best alternate world stories since the 2 part Star Trek story In a Mirror, Darkly because it went all the way in having a fresh view of established cannon. I would love to see DC explore more of the Multiverse on a regular basis. Why not? It can be good. Definitely watch Justice League: Gods and Monsters. I do warn that there is profanity and more violent than the previous DC animated films. This is more for adults.
Despite these small things, the film is very good.