I read that Scott wanted to do a movie more about the Engineers but thought people would prefer to know more about the Xenomorphs so went in that direction. I was personally happy with the movie, although I didn't find myself caring about any of the main characters, I liked seeing what David had turned into ... although so many questions, I'm looking forward to the third and final in the trilogy.
@rupert: I agree, I knew the movie would be full of stupid decisions when they entered a planet they knew nothing about without any protective clothing... I couldn't believe that.