The voice acting was distracting. I don't even watch NCIS and I only heard Mark Harmon. It seems to be a reoccuring trend in DC's animated movies by going with the bigger names instead of the better talent. Christopher Maloni in GL First Flight? Chris Noth, James Woods, Bruce Davidson in this movie? Dreamworks has been doing the same thing with their movies, putting bigger stars as the voice talent to little effect. Pixar however remains to use whatever voice talent they think is appropriate for the characters. Not to say that Marvel's animated movies are better. Daly rules as Batman though.
You are right, Batman basically killed two guys here. Owlman apparently had the choice of preventing the bomb from going off, but it would still be the equivalent of letting someone kill themselves. Johnny Quick was Batman setting someone up to die. Not entirely murder in both cases, but he still played an active part in their deaths.
Morrison's version of the Crime Syndicate story was far better. Owlman's plot was out of left field and didn't really seem like a natural progression of the plot.
J'onn having a relationship with Rose is weird, just because we've always seen her as a teenager. They just needed something to do with the character.
That said, after seeing "Rose" in this, I'm reasonably sure J'onn and Barbara Gordon would make a great couple.