It's no secret that this trilogy is about killing God. Even if the underlying story of the entire trilogy didn't spell it out for you, Pullman himself does in different interviews. He takes pride in it, in a way that to me seems like the way a bully will take pride in the way he beats down those weaker than he is. He seems to gloat about it, not just in his interviews, but in the narrative of the story itself.
I mentioned in my review of The Subtle Knife that the story itself sometimes lacked subtlety in the way Pullman told it, and now that I've finished the entire series, I can see that the entire trilogy lacks subtlety. It's not that the theme of the trilogy is a topic of discussion. There's no need to talk about what Dust represents, or what Pullman could be saying about churches in the real word based on how he portrays the church in the books, or even what the Authority could represent; Pullman states it bluntly in the books themselves, leaving no interpretation of events to the reader. He went into this series not with a story, but with an agenda, around which the story developed. It reminded me of the worst of Cory Doctorow's fiction in that respect.
I feel like it's important to note that I'm not attacking this series as a Christian offended by the ideas in this books. In fact, I'm an atheist, so it seems like this sort of story would be something I would appreciate. I just find the entire series inconsistent. If you're writing a series with an atheist agenda, why set up a world of spiritualism at all? Why use that as a backdrop for the entire trilogy, and go so far as to include a physical representation of people's souls? What's the point in building up that kind of world and make it the basis for the most genuine relationships in the books if you're just setting all that up to destroy them? Wouldn't it make more sense to frame the story outside of any religion, mysticism, or spiritualism to avoid that kind of association?
The books could have been much more impactful and interesting if Pullman had used more symbolism and ambiguity along the way. Aside from not alienating the group of people you might be trying to reach, the message would have been received more effectively had it been planted instead of being pounded into the ground. I noticed in one interview with Pullman regarding this series that he was surprised that there was more controversy over the relatively harmless magic in the Harry Potter series when his series was much more overt in theme. I think it had to do with the potential for those ideas to actually reach the reader. Not that J.K. Rowling is pushing an atheist agenda on her readers, but when you couch those kinds of ideas in a compelling, exciting, powerful story, they reach further into the audience. With Pullman's lack of subtlety, the tone of his story comes across as antagonistic, arrogant, and petty.
In the end, I just didn't find the series to be all that interesting. The Golden Compass was a good read that resonated with its potential, but each successive book became less interesting. It didn't help that each novel centered on a different world, thus breaking up the flow of the story that was established in the first book. I know the series is considered an epic tale comparable to The Lord of the Rings or The Chronicles of Narnia, but aside from Pullman effectively capturing the relationships between people and their dæmons, I don't see that at all. Even Lewis' Christian allegory isn't as brow-beating as this series is.