Shooting for different ratings, blowing through different designs and concept tests - this is all par for the course for every studio film. It also happened on Alien. A great expenditure was put forth to risk on Giger, who was Ridley Scott's muse, and Scott was no big name at the time, either. They went out on a limb.
In 2012, Prometheus was designed to restart what had become a massive franchise. The original script - all facehuggers, aliens, evil androids, etc. - was a somewhat safer bet. The final film, focusing even more on the Engineers/jockeys, was far less so. So while they did err on the side of caution with some stuff as was to be expected with restarting the property, the overall gamble of the larger concept - not just another Alien movie, but something far larger and weirder - was the real risk.