If the Engineers play the dominant role in the next film, he should have it where their technology is the mastermind, and that AI is a form of Trojan Horse designed to put a cap and reaction against the Engineers attempting to escape from their biomechanical enslavement (as was seen on Planet 4), which could be explained that this is the relationship between David and Protomorph. It is essentially the universe itself giving technology its own superintelligence and organic species - and the Deacons are a form of messenger, or evolution, of life itself. David was effectively an agent of the Deacons, the Engineers realized this as early as LV-223, and their sudden drive to kill humanity wasn't targeted at humanity itself, but the rogue state of our technology self-replicating and unleashing the ancient beast which had been trapped for who knows how long within the biotechnology that had enslaved them. It would be more like a symbiotic relationship, the Engineers on LV-223 commit themselves to service to the biotechnology in exchange for it consciously keeping the Xenovirus contained, and in return they get incredible abilities of intergalactic spaceflight and must create sacrifices. The whole thing is definitely more theological than scientific, and I think accentuating this would be an ideal nod to Dan O'Bannon and H.P. Lovecraft (and, of course, Giger's original concepts for the Jockies).