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I actually take the exact opposite approach, because if they had committed to it being an Alien prequel, a proper one, then it fills in a lot of the plot-holes. Like, "Why is it a silica based life-form that developed in an entirely different environment to Earth and who's sole means of reproduction is parasitism managed to become the dominant life-form in an eco-system" and the answer is that they aren't traditional life-forms, they're B.O.Ws, all the Aliens are Biological Warfare gone horribly wrong.
In terms of themes, this would be a pretty awesome addition to the Alien/Aliens series because that fits the theme so well. Corporate greed and military overkill being prominent in both, the idea that the progenitor race of humanity did the same thing helps to build on what starts as a simple-ish premise of extremely hostile alien life to a critique of intelligent life consistently developing self-destructive behaviour (I think I read somewhere the reason the awoken 'Space Jockey' goes on a killing spree is because he had an Alien egg implanted and that's why he was so furious, these stupid little monkeys had killed him. Although, now it doesn't make any sense except that they're all pricks and now they want to kill us but, GAH)
In that same universe the only other alien life displayed is the Predators and their society is going down a different but still destructive route, hampered by their own limited technology by societal demands. And even they misappropriate the 'Nuke' that is the Aliens, which as we've seen goes horribly wrong a few times.
As it stands, Prometheus's world as a standalone is too riddled with holes for me to properly enjoy it. A lot of the scenes are homages and takes on scenes from Alien but without the alien and replaced with psuedo-material which doesn't help with any of the themes because it doesn't make sense (and also my shocked disbelief that none of the scientists think finding worms on a planet IN SPACE is noteworthy, you just found alien life friends, NONE OF YOU ARE INTERESTED?). They needed to either commit to it being about the Giant dudes (which would likely have lacked the action scenes, flamethrowers, black goo) or commit to it being about why they died out (in other words an actual Alien prequel). This halfway trip, combined with scientists not knowing how a star chart works, is what made the film such a wash for me.