The movie was better in many ways than I expected. You have to feel sorry for Chris Weitz; he can't win. If he follows the book and makes it overtly anti-organized religion, he's going to offend the Christian Right. If he waters down the anti-Church rhetoric, he's going to be criticized for that.
He tries hard and manages to fall somewhere in the middle. The Church is replaced by the "Magisterium," and what philosophical underpinnings remain devolve to notions of Free Will and Independence. I think it's a case of "blink, and you'll miss the subtext," which may be cause for some of the criticism of the movie. I'm not a huge fan of the book, so perhaps was able to be a little more objective than those who had some investment in seeing the reproduction of the original to the screen.
Most of the critical discussion seems to be on the topic of the extent to which the movie tries or fails to live up to Pullman's lofty philosophical ambitions. Any perceived failure to match the ambitions of the book implicates the movie. However, it is more fair to judge the movie on how well it works on its own merit, leaving aside any debate about how successfully or not it translates Pullman's philosophy to the screen.
And on its own merit, to my mind, it succeeds. It is visually breathtaking, and effectively captures the bones of the story without sacrificing too much of the texture of the original narrative. The girl who plays Lyra - Dakota something-or-other, is perfectly cast. To my mind, she is more charismatic than the original. All the casting is very effective, with the possible exception of Nicole Kidman, who I don't think is quite cold and nasty enough. The CGI animals are all quite convincing. I felt the only place where the creators dropped the ball quite conspicuously was in the scene where the witches fly en-masse. This was one of the most memorable scenes in the book and was thrown away in a few seconds on the screen. They have saved the last two or three chapters of the book for next time, which made the ending somewhat more upbeat than it might otherwise have been. I found myself wishing that it was not necessary to film the battle scenes in the dark. The polar-bear fight, however, was extremely well executed.
In a side note, I found myself admiring Lyra's lovely Gap-style knit wear. Find yourself a Kaffe Fasset cardigan, sheepskin boots, coloured wool tights and a wooly hat, and you are equipped for heroic exploits in the North.