Yeah I know I'm flogging a dead horse but I came across some fan theories that I thought was interesting insights...
1) The Engineers (as seen in Prometheus) would visit various planets & if seen fit, would create life. They would then revisit the planet hundreds of years later to view its progress...
If they didn't like what they saw...war, famine, pollution, greed they would destroy the planet & possibly start the recreation cycle all over again.
Like the flood & Noah's ark.
David (in Covenant) discovered The Engineers were planning on revisiting Earth to destroy it & decided to kill off The Engineers before they could send a ship to Earth.
Even though David still had a hatred of humanity...he wanted the humans on Earth to destroy themselves at their own hands.
2) David didn't kill Shaw.
At the end of Prometheus, David is seen placing Shaw in a stasis pod but she is sick, feverish & wrapped in a blanket...apparently sick from a droplet of black goo in her uterus from her hurried caesarian operation.
In Covenant, all the experiments & flashback images of Shaw's vivisection was in fact David trying to save her.
And when he realised he couldn't save her as a human being, he then tried to change her into a human hybrid to stay alive.
Interesting theories. But why would there be so much unneeded deception in the storytelling in Covenant? "Oh, just kidding, what actually happened was..." Anyway I don't see them thinking it out well enough to save this franchise. They'll have to pull a miracle out of their asses if they are going to pull this out of the fountain of fail.