What I like about it is they changed the ending. It wouldn’t really be appropriate for Captain Atom to be the biggest hero in a Superman/Batman movie. It worked in the comics, though.
I also like the fact that they stuck with Ed McGuinness’ art style. It looks awesome in animation.
As with most straight-to-DVD animated movies from both Marvel and DC, the story is extremely compressed. I was disappointed that they left out the part where the Super family and the Bat family stormed the White House to confront Luthor about the whereabouts of Superman and Batman. That would’ve been fun to see animated. Also, we don’t see much of the dissection of the similarities and differences between Superman and Batman. That was a part of Jeph Loeb’s run on Superman/Batman that I really enjoyed. But eh, what are you gonna do?