I think one of the biggest points that people are referring to when they say that Snyder missed the mark is that he leaned too heavily on making Rorschach look like a cool anti-hero for the audience to root for when he's really a psychopath who believes his own nonsensical ideals. He also makes it painfully obvious that Veidt is "the villain" from the first scene we're introduced to him although that could also be Matthew Goode's performance, who I also thought was miscast. Also, giving Nite Owl II's suit a state of the art Batman-style look goes against the suit in the comics, which is supposed to be pathetic looking to match Dan's insecurities.
I think that the overall adaptation works but I can also recognize that, to paraphrase George Lucas, Snyder went too far in a few places.