Philip Pullman's His Dark Materials trilogy is one of the best series of books I have ever read. I won't try to rephrase the excellent synopses above, but I will add a few opinions of my own. Like SharQ, I don't think I would have understood the books at 12 as I understand them now. I would have seen a great fantasy adventure story with likeable characters, a fair amount of humour, cute animals, and a really awesome last battle at the end. I would have thought 'why does Lyra get Will, why can't I have him?' and I would have longed for a daemon. (OK, the last one hasn't changed. I think the daemon idea is pure genius and I wish it was true for our world!) At least - I think that's how I would have read the books. I shall come back to that in a moment.
Anyway: I didn't read the books when I was 12, I read them at the age of 24, and spotted the Miltonic references before Pullman started quoting him. I was also reminded of a short story by Neil Gaiman, the title of which eludes me right now, but it's in the Smoke and Mirrors collection, and if you've read it you will know which story I mean. Basically, the protagonist (I read it as Gaiman himself) is stuck in Los Angeles for a day while his plane is delayed, and he meets a homeless man who claims to be an ex-angel. He tells his own version of the fall of Lucifer, saying that Lucifer was kicked out of Heaven because he saw something he wasn't supposed to see: i.e., he would have uncovered a scandal. Gaiman's story has common ground with His Dark Materials, in that the Fall is seen as a clash of personalities or a simple fight for leadership/domination, rather than a fight between black and white good and evil. Although Milton writes in terms of good and evil, this aspect is clear in Paradise Lost too.
So: returning to how a child (or early adolescent) might view this book. Again like SharQ, I wonder to what extent these are books for children. Anyone who's seen Pullman's website and read some of his essays will know that he has an axe to grind, and is unashamed of it. And good on him, I think. Apart from the fact that critiques on religion are fascinating, I do believe that if there is an argument one way, someone should make it another way. Nothing should be beyond reproach. And although everyone has a right to an opinion, I can't help but cringe at the manner of expression some of his critics have chosen to adopt.
However. To put these kinds of questions upon children, is something I am less sure about. I have seen His Dark Materials in the 8-12 section of my local bookshop. And OK, maybe there are many levels upon which these stories can be read, and most children under about 15 probably wouldn't pick up the more serious aspects. But what if they do? It may vary from child to child, but I was personally not mature enough to handle serious religious questions until I was about 15, and I was quite a mature child. I was raised Catholic, and while I wasn't devout or even very serious about it when in my early teens, I tended to brush aside any critiques or attacks on Christianity, feeling rather uncomfortable - not disagreeing with them, exactly, but just not feeling able to deal with it either way, just at that moment.
Pullman has been quoted as saying he wants to kill God. Fair enough, but don't involve kids. If I am ever blessed with children, which I sincerely hope I am, I would be angry on their behalf if someone attempted to foist a religion upon them - any religion - before they're old enough to make an informed spiritual decision. And I count atheism in that.
But I don't want to end on a negative note. It may have been quite a major concern I was voicing, but it doesn't affect my opinion of the series. I think these books are brilliant. I found them entertaining, breathtaking, enlightening, educational, and very well written. I would recommend His Dark Materials unreservedly to anyone 15 or over, and without much reservation to over-12s. Parents: if you are concerned about these books, read them. You'll enjoy yourselves. If you're a Christian, remember that this is only one man's opinion, and, moreover, that the actual moral message of the books is probably something with which you'll agree. Pullman may have talked about killing God, but he has also said that Christian virtues are not exclusively Christian, but universal.