When Ridley Scott chose to go with a new mythology and story for Prometheus (based on writer Damon Lidelof's suggestions), it would have been much better if they had gone all the way and completely distanced their movie from Alien. No matter how good of a script they would have weaved, Prometheus could still never match up to Ridley Scott's original Alien. And for sometime during pre-production the movie supposedly didn't have anything to do with Alien. But the Alien brand is too big to ignore, so things from Alien ended up being shoehorned into Prometheus.