Didn't read through the posts so some others probably have the same response and theory:
I was dissapointed at first but after thinking about it more, it might be for the best.
Here's what I read somewhere. The Prometheus myth, as outlined in Metamorphoses, describes Prometheus creating a living being from clay in the image of the gods. From that, I think Ridley Scott was working on the Space Jockey mythos, maybe something to do with engineering living monsters. Maybe the Space Jockeys are the monsters. I haven't read any of the Alien comics so I don't know how they interpreted them, but I'm sure Scott hasn't either. He probably has his own ideas on their origins which clash with the comics, and fans from both sides would point out inconsistencies, etc. So the safest thing would be to use a lot of the main underlying themes, but not connect it to the Alien universe. In addition to that, he now has free reign and doesn't have to retcon it with all of the stuff that's already been established.