This may have been established already.

I don't read the Dark Horse comics, but I am a huge fan of the motion pictures. I don't descriminate, I love all the films from the AvP Universe and Prometheus. That being said I have a theory I wanted to run by this community. Been doing research and I know this has probably been brought up already and I might just be behind on AvP current events, but here goes.

This is purely speculative, but IMHO the most logical conclusion to the Alien, Predator, Engineer, Humanity conundrum is simply that the Engineers only created Humanity and that this was either an unsanctioned event or at least unwanted. The Engineers obviously don't grasp complete mastery over their genetic manipulation techniques. If they did, then there wouldn't be a heap of dead Space Jockeys on LV-223. I also find it highly unlikely that the entire species would be on the same page religiously, politically, scientifically, or morally. No civilization known to man ever has been. So, I personally believe that it makes more sense that the Engineers at the beginning of Prometheus, seen seeding Earth, are a more spiritual group that valued their ability to create life. I bring spirituality or religion into it based on the ritualistic nature of the opening to Prometheus. The robes, the self sacrifice, the whole sequence had a cult feel to it. Then you have the Engineers on LV-223. Developing biological weapons, wearing bio mechanical suits, preparing to wipe us out of existence. Stationed at what resembles a military outpost/manufacturing facility/temple and ofc launch point of our doom that was not their home planet. Even we were smart enough to park the Auriga in orbit around Jupiter in A:R. You don't do that unless you recognize the possibility for things to go horribly wrong and that's anticipating mistakes. So, the Engineers are not perfect beings without flaws, weakness, or lapses in judgement and therefore clashes of morality and ethics are a very real possibility in their society. Even the markers left behind on Earth could have been a warning. So, what about the Xenomorphs and Predators? Well, I personally like the theory that the Xenomorphs were a known by-product of the Engineer's technology or the actual result. The Trilobite's and The Deacon's resemblance to the Face Hugger and the Xenomorph are too much of a coincidence. I also lean more towards the idea that the Yautja have been present since the beginning or as long as the Engineers have been seeding planets. You could also entertain the concept that the Xenomorphs are a result of the Engineers unleashing the "black goo" on the Yautja. It would explain why they share the same color blood, why Predator blood partially neutralizes Alien's acidic blood, and why they are their ultimate prey and most honorable kill. 2000 years is plenty of time for what started out as survival, and the eradication of an infestation that was created solely to destroy your people, to work it's way into your civilization's lore, mythology, and religion. It could be what made the Yautja the way they are.