Okay, after sleeping on this:
PROMETHEUS Human Indoctrination Theory:
Engineers are a peaceful race experimenting with creation of life. They use magic black goo for experiments, and results are very different in different conditions. Sometimes they create humans like in the opening scene, but sometimes they create Xenomorphs, like depicted in the mural on that ship. They don't care much about humans, but they obviously keep xenomorphs under very strict control.
Unknown year, Wild Speculations: Engineers come across extremely violent, warlike civilization of Predators, which presents itself like a worst amalgamation of Roman and British empires. Predators see peaceful yet incredibly advanced Engineers as a perfect hunting target. Without having any weapons (the only alive engineer in the movie doesn't even take a gun from anywhere when he goes after Shaw), the only options for Engineers are to submit to Predators or to wipe their civilization out by unleashing xenomorphs on them. Even strong, violent and weaponized Predators can't stand the results of their planet being bombed with black goo/xenomorphs eggs. Engineers save lots of predator children and teach them to treasure peace and life over millenia. Military command of Predators, however, escapes and brings some of the xenomorph eggs with them.
Alien vs. Predator: They discover a planet which can sustain them, and it's Earth. It's also populated by very primitive Engineers, maybe even our herbivore ancestors. Predators know that Engineers are somehow involved in this planet's past, so they become our gods and teach humanity how to be brutal, violent, enjoy hunt and eat meat. Instead of primitive communism like Marxists used to call our initial state, strong leadership based only on power, violence and free market shapes human societies. Predators also use humans to build pyramids in which they place xenomorphs' eggs to train against them for whenever the time comes for their revenge. Predators also know where the black goo came from, and that's why they teach humans the star map they find in Prometheus: if there ever shows up any ship from there, you're DOOOOOMED.
Space Jesus, around year 0: Everything goes according to Predator's keikaku* until Engineers stumble on Earth and see that not only the violent race they thought they now completely keep under control somehow managed to recreate itself, but they also found proto-engineers and taught them how to make weapons and be as violent and brutal, including latest gift from Gods the whole Roman Empire enjoys so much: gladiator fights. Engineers are outraged. They send their emissary, Space Jesus, to Earth to try and teach humans how to be peaceful and love each other and that Predators are not Gods but actually Demons they shouldn't listen to. Humans, however, not only brutally kill Space Jesus, but also let Predators know about Engineers showing up. Engineers are scared and hopeless, they decide to use their last option: bomb Earth with black goo and xenomorphs to kill both Predators and predator-lite humans. They are, however, slowed down by their own love for life and are very reluctant to kill species which is their exact DNA match.
This gives Predators time to prepare for war, and at some unfortunate for Engineers moment, Predator fleet descends on LV-223. Engineers don't have any weapons, and don't keep xenomorphs just sitting around, so they are slaughtered within minutes. Remember those running holograms from Prometheus? We never see what they were running from because those were invisible Predators. Why were they running to the room with Xenomorph mural and black goo? To sacrifice themselves and unleash xenomorphs to defeat Predators. But they failed, and were all brutally slaughtered, all but one, who hid in a pile of corpses. Predators read the map to Engineers homeworld, or maybe even tortured one to give up information on its location and took their fleet there, which also leads somehow to one of the Engineer ships falling down on LV-426 (we don't know its origin or its destination, but it happens around this time). The only surviving Engineer is severely wounded and goes to medical pod/stasis capsule combination in hope that he will soon be awakened by his own brethren.
Year ~2000, We don't know what happened, but here are some more speculations:
(AVP

Predators no longer live on earth as gods, but still use old pyramids for their ritual xenomorph killings. (Predator 1&2

They also consider humans advanced and violent enough for their skulls to be worthy hunting trophy. (Predators

They also control some other planet and use it as a more pure, safe hunting ground, probably for their young. There are also 2 types of Predators: good old violent ones and those who were raised by Engineers, and they don't like each other.
Engineers are nowhere to be found. They never came to figure out what happened to LV-223. They never rescued their ship/team on LV-426. For all we know, Engineers are extinct except that one guy sleeping in stasis pod.
Prometheus (2092): humans find LV-223 and last Engineer. He sees humans and thinks they might have been saved, but something David says gives out clear indication that they are Engineers only by DNA, but Predators by their culture. Last Engineer knows that it means only one thing: Engineers are extinct and Predators won. He smashes humans in his blind rage, and wants to do the only thing he can still do - destroy Earth to avenge his, can't even say race since they are the same race as humans. Let's say, to avenge his civilization and to save Universe from evil humans, but he fails.
Alien/more movies (22nd century?): humans come into contact with xenomorphs ship on LV-426 was carrying and all that stuff happens.
More speculations:
2154: Bad violent brutal humans try to kill off peaceful Navi's for personal gain just like Predators taught them.
40000: God-Emperor is some kind of Engineer and is the last hope of humanity in the battle to wipe out every other race as well as heretics and mutants. Predators and Navi's are already extinct. Space Marines are Engineer-human hybrids: they are huge and strong as Engineers, but still have hair sometimes. Chaos is self-aware black magic goo.
*keikaku means plan