Having finished The Subtle Knife, I hardly know what to say about it. It's extremely good. Just like The Golden Compass, I read it fast and enjoyed it a lot. Just like The Golden Compass, it's a young adult novel that respects its audience rather than talking down to them.
Just like The Golden Compass, there are definitely elements in which the Church is challenged. I feel reluctant to mention that, because it's the kind of thing that may turn people off to the book (of course it's easy to forget, especially for those of us that live in Alabama, that many people are turned off by books that promote the church). I still think it's a very good story that I would recommend to people whether or not they are Christian, because 1. good storytelling should be available to everyone, and 2. you can take it. Seriously. The challenges to the Church are not that bad, and if they cause you to question things that people have done in the name of God, things people still do in the name of God, would that be such a terrible thing?
Of course, I also want to reserve judgment until I finish book 3, because the books leave you wondering what the outcome will be.
But this isn't why I don't know what to say. I don't know what to say about it because discussing the plot gives away so many elements of The Golden Compass, and the moments of revelation in this series are so stunning, it would be a shame to spoil any of them.
So, what's safe to say is - Lyra learns more about Dust. She travels between worlds, but the reasons for the different worlds are supported by current theories of physics (which makes it a lot nicer for me than, say, popping through paintings). She meets a boy named Will, and before long he's just as important as Lyra. There are more witches, which is a good thing. Someone dies, and it's heartbreaking.
Overall, small questions are answered and big questions remain, and it's sometimes difficult to tell which adults are good or evil, although I suspect that anyone who is decidedly for Lyra is good, and anyone who is against her is evil. There is one adult whose loyalty to Lyra is not clear, and everyone keeps trying to guide her to him, but I'm just guessing that based on his past action, he's no better than the adults that are clearly against her.
See what I mean? I can't tell you anything specific about these books without spoilers. Read the books! Don't watch the movie! They are page turners, and they are exceptionally well written. You won't regret it.