I've used the heading SPOILERS to point out this whole article could ruin Prometheus if you read it so you've been warned. Ridley Scott while speaking with The Wallstreet Journal's blog Speakeasy he gave a small tidbits of details on Prometheus. Confirming that the Alien DNA is in the film stating "The last eight minutes of the “Prometheus” story evolve into “a pretty good DNA of the ‘Alien’ one".
This news leads me to believe there is a possiblity that Ridley and Fox could be considering a sequel which had been in the original plan. While setting up the alien world with Prometheus the next installment very well could end up being the Alien prequel that was originally intended. When the Alien prequel was originally announced there had been plans for two movies that would explain where the eggs, ship and Space Jockey came from. It's unknown how much of Prometheus will actually explain if anything of the mythology/origin of the aliens. I wouldn't be shocked if the film ended with a cliff hanger leading into the second film, if that plan still exists.
I had my doubts how they could make one origin story into two movies but establishing the human world, androids, the company's motives and colonies would be the first step, the second explaining the origins of the aliens. This of course is all speculation but it's going to be a massive treat for Alien fans like myself it does turn out this way. There has also been talk that Prometheus very well could be told from the prospective of David (Fassbender), one of the androids in the film.