Dear Mr. Pullman,
You wrote a great series. The plot's pretty good, but it's only "pretty good" because you share a genre with Jo Rowling--in any other genre I'd call it "excellent". You violated the tabloid weird rule ("Either the FBI is hunting the escaped mutant from the genetics lab, or the drill-bit has bored straight into Hell -- but not both at once in the very same piece of fiction") without losing consistency, which is fairly impressive. I adored the anti-religious bits, but I would. You got me to fall in love with Will and Lyra, which is pretty impressive for non-intellectual characters. I now consider you someone who doesn't get enough attention for his work.
(Incidentally, Pullman: Your book is not merely anti-Church; it's also anti-religious, otherwise you wouldn't have written the Authority's backstory the way you did. Be proud of what your book is, not ashamed of it!)
You need to learn that there's nothing wrong with a happy ending. Really, I swear there isn't. After you put your characters through hell, at the end of the last book it's alright to give them rewards tempered only with the pain of the journey taken to get to them. You don't have to give and then take away. I'm sure you have all sorts of thematic reasons to do it, but they don't change the fact that it tampers with my enjoyment of the story, which isn't a good thing. I was spoiled for the ending, so I could prepare myself; if I hadn't been, I might have set the series aside and never read it again. Which I never do.
That's basically my only quibble. Pat yourself on the back--but put a thumbpin between your fingers before the last pat. Cause that's what it's like.
Anyway, I'm not gonna do what he did. Wide Awake will have an ending where all the surviving good guys get to be happy. I swear it.
Will/Lyra is now officially added to my ship list, but I always knew it would be. I'll probably slot in a re-read after Potter; I can sense a whole lot of shared influences that lead to plot similarities, and I want to see how many I can elucidate.