After listening to the screenwriters' commentary, I like this movie a lot more. Apparently, Ridley cut several scenes explaining David's motivations. He was experimenting with the organisms hoping to find something that would extend Weyland's life at the expense of everyone else.
Well, he did cut them. I can't have an opinion on a different version of the film when none exist. As it is, Prometheus is a disappointing mess, and I don't really care if Ridley Scott had good intentions.