Babylon 5... Good series, at least seasons 2-4. I don't think this is what Ridley is doing. I think the overarching plot is the Engineers created humans and Xenos. Humans proved disappointing, Xenos were supposed to erase them. Seems to me, it would have been simpler to drop something large from orbit, nuke the planet, or just spray a part of it with black goo and let twisted nature take its course. How we end up back on LV426 is not clear. If the derelict is only a few decades old, that will be disappointing. If it turns out to be Shaw in the pilot's seat, that will be silly. I see lot of ways these sequels can turn out badly, a lot of ways they never get made.
I wasn't being too serious with the B5 Shadow War reference, but the Shadows were pretty creepy when it came to their biotechnology.
I still can't get my head around any circumstance where the Xeno was created to kill humans. The only scenario that would remotely seem feasible would be if the Xeno's were created to take out a particular faction of Engineers, and they want to use humans as a test bed to see how effective they would be.
Personally, I think there are two possibilities why they created humans.
1) use as incubators and food for the Xenos.
2) The back goo was meant to weaponized us to possibly fight the Xeno's. Our final form was meant to be.
Straczynski is a fan of Lovecraft and the B5 elder races all owe at least something to Lovecraft. The Shadows do this most blatantly, I think. And they had creepy biotech and servitor races like the Drakh.
We don't know enough about the Engineers' mindset or motivations to say what makes sense to them. Someone around here mentioned the idea of a war between the Engineers and Predators. That could be an interesting thing, and the possibility is supported (albeit indirectly) in the canon of the films. Both the Engineers and the Predators have a valid claim on the development of humanity. Predator 2 pointed out that the preds have been visiting earth for a long time, and AVP goes even further. Allowing events of AVP into the Alien canon is contentious, but I'd say, you can't really deny it. I think it makes sense to accept that they all share one big, not-so-happy universe.
As far as making humans to be food/incubators for xenos, that seems unlikely. What we're given in Prometheus indicates the engineers - At least some of the Engineers, wanted humanity to develop and thrive. There is no reason to make humans as incubators because xeno eggs or the ampules could be seeded on any world or installation where the engineers wished to eradicate or modify a particular lifeform.
As for what humanity was supposed to become or what the black goo was actually supposed to do, the dog-men are one possibility.