There's a scene in the theatrical version of The Fellowship of the Ring where you see a shot of Boromir in a boat looking peeved; and later, as he's dying, he seems overly enthusiastic when Aragorn say that he will save 'our' people. The meaning of the two scenes really only becomes clear in the special edition; just before the scene in the boat, Aragorn and Boromir argue, and Aragorn insists that he will never take the Ring near 'your' city. Everything falls into place with the addition of this scene. Boromir is tense because of the argument, and because he believes that Aragorn's refusal to accept his lineage will lead them all to doom; similarly, when Aragorn says 'our' rather than 'your', Boromir understands that Aragorn has finally accepted his fate: and that gives him hope in his last moments. There's an entire level of narrative and interaction between these two characters which is absent in the theatrical version, and which is essential to proper appreciation of the film.
The Golden Compass is full of these moments, or rather, full of telling omissions. It's not that it contradicts the details of Philip Pullman's excellent novel, so much as it leaves out details which lend sense to the rest of the film. Everything on the screen — aside, perhaps, from the readings of the compass itself — is great: the acting is excellent, the music is good, the digital effects superb; but somehow the whole amounts to less than the sum of its parts. It suggests the story, rather that embodying it.
If ever there was a film which truly needed an extended director's cut, this is it. It should be, and still could be, a magnificent film; but we'll have to wait and see.
(I'm looking forward to the start of the next instalment — assuming it gets made — since it should open with Roger being killed by Asriel. Maybe too bleak a way to end a film, but an awesome way to begin one. Bwah ha ha.)