I really liked Belle Sauvage and Secret Commonwealth.
I agree that the children in school etc were disturbing. Yet so real and plausible. I liked the flood, I found the narrative kept you going as though you were racing along with the river. It also felt reminiscent of the Odyssey or others of that ilk, an epic poem. I loved the snippets of strange things they met as they went. We'd been introduced to the concept of ghosts and ghasts being real in His Dark Materials but not seen how close and real other magical realms could be.
I hope that is further explored in the final Book of Dust. There must be a reason for the big focus on the Secret Commonwealth. I hope we explore more of Oakley Street too. I find the politics interesting and look forward to seeing how that pans out. Will there be political reform that leaves us feeling that the people and characters we love will be able to live in peace? When we left Lyra at the end of Amber Spyglass she may have had a victory against the church but they were still powerful and we knew her peace wouldn't last.