In my opinion the problem with Prometheus (and its sequel) is that it's Ridley Scott's movie. Alien wasn't his. It was Hill's, Carroll's and Giler's movie - not even O'Bannon's. Those three took his script (which really wasn't very good) and polished it, gave it the character. That's basically what they say in bonus features, but I agree - I've read O'Bannon's version and final version and they're miles apart. Hill, Carroll and Giler might be soulless, cynical, money-grabbing Hollywood leeches, but they sure knew how to write a good story.
And so, Scott didn't intervene with the script while making Alien. He took what he was given, no questions asked, and just visualized it. He's a great visual artist, but when he wants to tell his own story, we get Prometheus. Scott needs a good producer to tell him what works in terms of story and what doesn't.