This is definitely the second book in a trilogy. It does not stand on its own well, unlike the first book. Where The Golden Compass took place in a world somewhat like ours, but clearly magical, The Subtle Knife is set largely in our world. It really establishes the way the worlds work together, and connects the fantasy elements of the story with faux science (connecting multiple worlds to quantum mechanics, and falling back on the old science fiction standby of science-as-magic). Not that this is a bad thing. It’s just a thing.
I’m not sure if the religious message was better worked into this one, or if I was just expecting it. Either way, the delivery of the themes seemed to work better in The Subtle Knife. My feeling is that Pullman didn’t want to scare readers away by leading in too strong with it, so he backloaded the first book with the Church-as-bad-guys stuff. Consequently when he did include it at the end, it seemed more heavy-handed than necessary.
This book is a smaller adventure than the first and third, mostly just setting up The Amber Spyglass. It is still delightful fantasy, with fun ideas that are explored, but seems the weakest of the three.
Oh, also, I think the Subtle Knife (the titular artifact) is one of my favorite magical items in fiction. I won’t spoil it, but Pullman’s descriptions of its magic are wonderful.