The Amber Spyglass is a frustrating book. It comes so close to being as dark as the His Dark Materials trilogy title implies only to take a turn into the power of love.
Pullman has a bad habit of setting up a plot twist at the end of a novel only to go in a completely different direction in the sequel. Some spoilers follow. In The Subtle Knife, Mrs. Coulter is told that her daughter Lyra will be placed in the position Eve and make a decision that could cause a second Fall from Grace, and Coulter declares she will kill her daughter to stop this from happening. Mary Malone is told that she is to play the serpent to Lyra. Instead Coulter makes a heel-face turn that strains credulity and Malone spends the book befriending a race of creatures that roll on wheels. In makes me wonder what the plot for this novel was in Pullman's mind when he finished The Subtle Knife.
There was a lot I enjoyed about The Amber Spyglass as well. I liked the aliens on wheels and their sailboat bird enemies. The whole underworld quest was quite interesting, although for some reason the bold adventurous Lyra and the tough as nails Will gradually degenerate into the sweetest children ever. The great war ended up being not Good vs Evil, but rather Freedom vs Authoritarianism, which was refreshingly different in a Fantasy novel, even though the leaders of the freedom fighters all have aristocratic titles which is a tad anti-revolutionary.
Like a lot of vehemently anti-religious people, Pullman seems to be a disappointed and frustrated religious person. He wants angels to be forces of good, he wants the wicked to find redemption, for the Kingdom of Heaven to be realized in the real world. In other words, he wants to immanentize the eschaton. That is what he leaves his characters working toward, although the ending is more bitter than sweet.