I think when making a movie with "ties to Alien", people were expecting a very different sort of film. The original Alien was essentially a "slasher movie in space" and this theme was carried out to each one of the sequels. The Predator movies also had this slasher theme where the characters were hunted down until there was only one of two left, even the AVP movies (no matter how much people hated them) preserved this element.
Prometheus was very different, however, there were very few characters the audience actually cared about and the majority of the cast was cannon fodder for monsters, etc. Also due to poor editing, dead characters magically resurrect themselves back to life in that magic time between Fifield's attack and the confrontation scene between Vickers and her father. All in all, Prometheus could have been a great film but the ties to Alien ultimately held it back from being what it was aiming to be.