I'm still convinced that the reason a lot of people disliked Prometheus is that they were expecting something that Ridley Scott explicitly said it was never going to be. He's tired of Xenomorphs and wants nothing whatsoever to do with them anymore, which is the whole reason he brought on Lindelof in the first place.
I don't know, the
Alien(s)-style xenomorph bas-relief on the temple wall, the bioweapon jars arranged in a similar manner to the xenomorph eggs, the geologist gradually changing into a xenomorph, the giant facehugger, and the modified xenomorph baby at the end are an odd way of showing that he wanted nothing to do with them at all.
I would have been fine with either a true prequel to
Alien that focused more on the Xenomorphs or a story that focused entirely on the Engineers, but what we got was sort of a hybrid of those that seemingly couldn't decide what it wanted to be, and so it ended up giving short shrift to both aspects of the story and was unsatisfying as a result (IMO).
I would have much preferred some greater background be given to the society and objectives of the Engineers rather than the utterly ridiculous action sequences we got toward the end. Or to Tweedledum and Tweedledee meandering through the alien ship that the world's most incompetent geologist mapped himself, while the world's worst biologist pets the hostile space cobra with inevitable results. Or to Old Guy Pearce visiting from the set of the LSD-inspired monolith sequence in
2001, complete with terrible 60's-era prosthetic work.
I know they can (and most likely will) greatly expand on the story of the Engineers in the sequel, and I look forward to it, but when you sell the film as telling their story and then don't adequately deliver on that premise; nor do you effectively set up the events in
Alien; nor do you make a well-constructed and self-contained story that stands on its own merits, it's more than just disappointment at the lack of more xenomorphs that's the problem.
