As I recall, the biggest problem was that you can't fit the events of the first book into a 2 hour movie. There's too much lore background to explain, and the movie skipped through it to get to the armored bears. They also chopped off the ending because focus groups didn't like it.
It'll be interesting to see how His Dark Materials handles the commentary as it gets more explicit. It didn't shy away from making the Magisterium moustache-twirling baddies.