The reason for the changes to the Ithilien section are expained in some detail by Phillipa Boyens on the third disc of the extended DVD. Surprisingly, I found myself nodding agreement to most of them. To paraphrase: for dramatic purposes it seemed necessary for Frodo to encounter an obstacle in Faramir, otherwise he gets a more-or-less clear run to Cirith Ungol. To me, the changes make better sense on the extended DVD, with Osgiliath being introduced beforehand via the extra Boromir/Faramir/Denethor scenes.