Script
Loss of Theoretical Phyics 
Will Enters in NL
Father MacPhail
Stoppard's Script Scrapped
Sir Tom Stoppard is no longer writing the script for His Dark Materials. You can read more about this development here.
With that in mind, this was the state of play with the script as we previously (note the now defunct use of present tense) knew it. It is possible that some of these changes will be kept by Chris Weitz's version of the screenplay - or, of course, none of them could happen at all.
Washington Post, 14 December 2003
'Stoppard has completed a screenplay based on "The Golden Compass" -- it took three drafts, he says, and he was asked to lose some of the theoretical physics behind Pullman's concept of parallel universes, which he'd found fascinating -- and has started on a treatment of the next two books. Among other changes, he brings Will into the story at the end of the first film and he introduces a major villain, Father MacPhail, much earlier than Pullman did.'
This should be added to the previous quote - Bob from the Washington Post writes to allay the fears that Dust might be removed from the His Dark Materials movies: "I think what Stoppard meant was that he was intrigued by the REAL-LIFE physics behind Pullman's imaginary worlds... and my impression is that he'd played up this much narrower topic because of his own interest. I got no hint of any threat to the centrality of Dust in the story, and I doubt very much that Pullman -- who's read the screenplay -- would have been so positive about it if that concept had been mangled."
So, Dust ain't going nowhere. Big sigh of relief all round. Seems that Sir Tom has been expounding on the parallel universe theme a little and has had to cut down on it - he sounds enthusiastic about that sort of thing so could very well have got carried away and made things a little too heavy for the kind of audience Newline is aiming at.
An interesting one this. Most of us feel that NL should just be Lyra's story, but it seems that Stoppard has decided (for whatever reason) that Will must be introduced towards the end of NL. Now, there's a number of ways they could do this and I'll quickly elaborate on just a few:
1. Will's story is intercut throughout NL, culminating in Lyra bumping into him as she does in TSK - the story ends there as they stare at each other.
2. (With thanks to Gabe) Same as above, but continues along to the scene where Lyra asks the alethiometer about Will - it replies 'He's a murderer' and the first film ends.
3. Nothing about Will throughout NL, Lyra bumps into him at the end as before. When TSK starts, Will tells his story so far to Lyra and we see it as flashbacks.
Just a quick reminder for those of you who might be unsure - Father MacPhail is the high-ranking Churchman who orchestrated the plot to kill Lyra with the Bomb, he was involved in the action with Mrs Coulter in Geneva.
This shouldn't really have that much of an effect on the story - presumably Stoppard means that he'll be introduced in NL, though in what way or how much about Lyra he'll know is, well, unknown. Perhaps MacPhail could be involved / in charge of Bolvangor too? This one's hard to call at the moment, it could be a good move to have a major villain early on and develop his character more than in the books, or it could just draw attention away from the important events in NL and be a distraction. We'll need to know more before we can judge this one.