Now that I've read the added lab scene dialogue in the novel, one thing I noticed regarding David creating the Aliens in the film vs. them pre-existing in the book:
The egg that David shows Oram in the book while explaining it was created by the Engineers before him actually appears in the film. I noticed it on my second viewing. He walks up to it in the foreground (at which point it's cropped mostly out of frame) and removes one side of it, then afterwards it is seen behind him, the side removed and a Facehugger inside. He never addresses it with dialogue, and it's never shown clearly, but it's there and he interacts with it. Seems the scene from the book, in which he states the Aliens are ancient, was probably filmed for the movie then cut out.
Even before reading the book, I kinda felt like there was a bit of a jump at that point in the film, as though something had been removed. Did Ridley come up with David being the ultimate creator during the editing process?