A...greater...threat?!
There's a few ideas that come to mind. One must be mankind. Prometheus was the first privately funded deep-space exploration mission, if we are going off pure Prometheus lore, so the Engineers must foresee mankind developing the capability and capacity to explore and colonize new worlds in mass scale. Perhaps that is a threat over their dominion?
Another idea is another species, represented by the different style of ship shown at the beginning of the film and used in an Easter Egg space battle in Aliens: Colonial Marines (like it or not, FOX says it's canon so clearly they mean to depict two different races). Possible civil war or perhaps the original Space Jockey is NOT an Engineer but something else completely?
Finally, my personal hope, is that the greater threat is THE PREDATOR RACE, BECAUSE WHY THE HELL NOT?!
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Obviously there are reasons not to go this route, but I don't see it as an impossibility. FOX knows there is this unavoidable parallel between their two fictitious species, thanks to the comics, video games and movies. Now, knowing Ridley, he won't do this unless forced to and at that point you're probably looking at a different director if FOX won't budge.
Ultimately, I would like that route because I really like the Fire and Stone series and would love to see it made into a 2-part film series or short TV program (like hour long episodes), despite the flaws and speculative nature (but it would be able to be flushed out since the BIG QUESTIONS will have been answered at the Prometheus film series conclusion).
One final thought... what if this was a weird Aliens: Nightmare Asylum [Book 2] variant using Prometheus? Corporal Hicks knows where I'm going with this... perhaps the Xenomorphs that were "engineered" were created to fight an indigenous version of the very same creature??? Aliens Genocide with Engineers trying to control their creations?