I thought it was fairly simple:
--advanced life forms spend generations seeding life on planets with their brilliant life-generating RNA technology. They dosed the "primordial soup" with what we already understand to be the RNA world of early earth. They leave some rando maps in case their little science experiments ever get smart enough to seek them out.
--Turns out, their little laboratory base that holds their vast knowledge, as well as their active experiments (yes, this is already a bad idea. Us humans already know that you put real barriers between dangerous active experiments) gets overrun by their worst, most ambitious, most perfect attempt at generating life.
--They trap the critters as best they can and hibernate themselves (it's what all the humans have been doing in these movies, anyway), but when that dude realizes that humans have arrived, it activates their emergency safety protocol: These things can't escape, so wipe out all humans....uh, with these things, or something. lol.
When the Nostromo finds the crashed Founder ship in Alien, so much of that crazy architecture and gothic insanity is begging for some sort of explanation. These aren't "just some terrifying creatures." ...how the hell did that thing get there? We're already given the premise that those dumb miners are dealing with an extremely advanced, vastly ancient alien civilization. It's all already there, and I don't think Prometheus is at all far outside of what Scott wanted to do with that lore. Remember, he produced, directed Prometheus. If he didn't like Lindeloff's treatment of the story, then he wouldn't have supported it. All of the design and plot of Prometheus is literally plucked straight out of Alien. (and into Covenant....not that I think Covenant is that great or anything, but it's good enough).
I think people just bitch that it's not what they wanted the story to be.
You guys want to bitch about one of these movies? Focus on Alien Resurrection.