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.
Well, that's why Scott kept saying it wasn't an
Alien prequel or sequel, it just "shared some of its DNA."
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.
It all boils down to how you interpret it. The way I read the film, these people
thought they were leaders in their fields, but the only one who actually even remotely was was Shaw. Everyone else was an incompetent hobo hauled off the street by Weyland, because he didn't give a shit about the mission, he just wanted immortality. "Pfft, as long as they get me there, David can do the rest."
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.
I guess it boils down to what you're looking to get out of the film. It is such an unsettling film. I'm a huge fan of Ridley Scott but I don't think he's ever done anything of this magnitude. The attention to detail, as seen in
Alien, and the relentlessness of the themes, as seen in
Blade Runner, are there. I don't think
Prometheus beats either of those films as Scott's "best," but it's definitely one of his smartest films.
Think of how you approached love, relationships, when you were young. You went all-in with this naive, idealistic sensibility, and then you get in over your head, and you wonder to yourself, "What the HELL have I done?" You try to do your best to carry on, soldier forward, and find some meaning in everything ... and, nope. Nothing.
Then you meet "God," your creator, the being responsible for your existence, and you ask God why everything is
so incredibly messed up. And God ... gives you no answers, shows nothing but pure hatred and then sets out to express that hate upon your entire race and it's incumbent upon you to prevent that disaster.
Fuck, now I need to go watch it again tonight.
Edit: Time to start talking titles.
Prometheus and Prometheur?
Prometheus 2: Genetic Boogaloo?
2Pro 2Metheus?
Edit 2: To further clarify, when Ridley Scott goes sci-fi, his films aren't necessarily about telling a compelling story.
Blade Runner is boring as hell until you look at the design, the art direction, and the themes, and you realize that it isn't a boring cop movie with pretty pictures, because there's so much going on beneath the surface -- the subtext is ridiculously rich. Even in
Alien, too, because that film's about a gigantic penis monster raping the shit out of a crew of ineffective fools and only the woman can repel it.