I have some thoughts on 'fixing' this movie.
1. David and Charlize whole "I am your father!!!" is much more in the background.
2. The scientist adjustments from the commentary happen, and they do not take off their helmets, come the hell ON.
3. Instead of being emo and a total dick, Holloway is happy stupid drunk "I found the foundations of LIIFE!!!" and it pisses David off, resulting in the poisoning.
4. Instead of being upset and scared by her creepy fast pregnancy, Noomi is totally thrilled that at last she can "create life."
5. She and (reluctantly, because he thinks it will kill her) Holloway and (because daddy) David are pitted against Charlize and the rest of the crew, who have seen what happens when whatever is in those caves mixes with humans.
So that is at least some conflict that I think is more compelling than the "god, monsters, something...?"
I know, it could never happen because of politics around reproductive rights are so crazy, but it would be interesting.