It helped that it was very clear that all the actors loved what they were doing and wanted to do it justice, even if they were given the wrong material (Rorschach) or not enough (Laurie and Sally).
Things that annoyed me
* The gratuitous violence. It was pointless and unnecessary and detracted from all the good things about the movie. Someone needs to smack Zack Snyder until he grows up.
* The gratuitous 300-style zooms and pauses. See above.
* Sally and especially Laurie getting shafted for screen time and development.
* The very end. They lost a huge amount of the ambiguity that gave the comic's ending its resonance. What stood out for me most: having Laurie parrot Dr. Manhattan's "nothing ever ends" line accomplished none of the same effect as having him give it in response to Adrian seeking his approval.
Things I have mixed feelings on
* Rorschach. The actor did his best, he had some terrific moments, and his death was spot-on perfect in a way that the rest of his characterization wasn't. But he was written and directed as cool too much. Where was all the stuff about him smelling bad? And his flashback origins scene was cringe-worthy.
* The score. I know exactly what they were trying to do with the pop culture onslaught (it does exist in the original comic, you know), and I think that if they'd used an ounce of restraint and a dash of subtlety it could have been great. Most of the time, they didn't. There is one exception where I disagree with absolutely everyone else I have ever seen talk about the film. I'll get to that below.
* The main change to the ending. It was extremely cleverly done, but the symbolism is too heavy and introduces extraneous thematic elements that don't really fit with the original.
Things I loved
* Everyone's acting, as I have said.
* Doctor Manhattan and just about everything they did with him; Ozymandias to a slightly lesser extent.
* A small thing: in the flashback to the Comedian's attempted rape of Sally, they briefly remembered that they were in a movie, not a comic book, and used it to their advantage. Before he turns to go into her dressing room, Eddie looks right at the camera and gives us a knowing smile. Perfect.
* Here's my heresy: the "Hallelujah" sex scene. I was cringing at descriptions of it, I was completely prepared to hate it...but then it actually started and it was nothing like I thought it would be. We've been conditioned to see "Hallelujah" as the generic angsty love song of sadness and woe, but it wasn't originally written that way. In this scene I felt like I was hearing and seeing the original intention of the song as a self-mocking but appreciative nod to human stupidity and silliness in life and love for the first time. Laurie and Dan had just gotten horny from heroics, they were flailing around and setting off buttons, a more faithful to the original than usual "Hallelujah" was playing (was it Leonard Cohen's original?)--it was genuinely funny. I doubt Zack Snyder, with his total lack of subtlety, intended it that way, but someone, somewhere along the line, did. I just can't believe that was intended to be serious and dramatic.
* The pretty. Oh, the pretty.
* Everywhere that the richness of the original material shone through. I felt like despite the screw-ups, there were a lot of places where this happened, and they were really breathtaking. I couldn't say if Watchmen stands alone as a good movie; I doubt it. But as an extra treat for someone who's read the comic, it was amazing.