What about Elizabeth Shaw?
Did anyone ever explain what would possess her to repair David? I mean it's not as if there hadn't already been indications that the David droid was, ah...not functioning up to safety specs, shall we say? Restoring David was suicidal and inexplicable.
I agree that as far as I'm concerned, the entire Aliens franchise is 2 movies, Alien and Aliens. When they made Prometheus, they incorporate bizarre ideas that don't fit into the Aliens universe at all well, like the Engineers using self-sacrifice to seed worlds with life. I'm sorry, that's about as sensible as a box of rocks.
I will say that all the way back in the 80s, I was pretty sure that the xenomorphs were artificial, somebody's bioweapon. That idea doesn't bother me, but the way they seem to be going on it makes no sense at all.