Although I agree with nearly all of the above hypothesis just let the "ancient aliens" nonsense stay dead, let David, believing itself the creator, discover the LV-426 Derelict exactly as it is far predating any form of humanity. Let the revelation fully unravel the Artificial Intelligence, he's not truly unique as he currently believes, it's all happened before, the "Perfect Organism" combination of organic and synthetic existed before and it's the Alien.
That's great. I really like the idea of David discovering he's not the god he believed himself to be. If this could tie in with the Engineers being part of some kind of corporate hoax then I'd be happy. Something that would destroy the "ancient aliens" nonsense and at the same time add more to how big the conspiracy within Weyland-Yutani is. I think I wrote it in a previous thread before, but I'd like it to come out that the Engineers are like "Replicant" type things that were sent in advance, by WY or another company, to pre-terraform worlds. Some discovered a crashed Space Jockey ship and decided maybe there's more to the universe and tried to become their own thing. Perhaps there's controversy about sending these somewhat sentient beings into space to colonise worlds on the quiet.
They should explain that everything is an Ancient Conspiracy
. So the Engineers are genetically engineered super humans, created by Weyland Yutani in the future as part of a secret terraforming project using Space Jockey technology, which was obtained from never-before-seen artifacts (not the Derelict) made by the Mala'kak species: Non-carbon based life forms similar to pachyderms, capable of generating symbiosis with machines, sometimes altering space-time around them or even reality itself. They're not ancient, nor entities from a distant future. They just exist above everything.
Now back to the "Replicants", the experiment got out of control, triggering a transhumanism event were the Engineers become an unstoppable Posthuman civilization. They can perceive time in a non-linear way thanks to Mala'kak bioengineering. This makes them able to interact in the past, present and future. We are our own gods, and yet we are biased by our own arrogance. Building better worlds is our motto.
Then, our creation David discovers that the Derelict has been on LV-426 for millennia with the original Alien, which makes David another Ossian
I'm looking forward to see that villain ego fall from the highest
Plus, in this "what if" scenario there might be some kind of City in a Bottle
, so to speak. A background of the City Noir
kind, which look like an in between Cyberpunk
world; where the Engineers are being born. A setting like the one featured in the movie Dark City. Or even something like Blade Runner meet BioShock