How They Could've Won Over Both Prometheus Fans and Haters
My contention is this movie split the baby and killed it with audiences because by writing Shaw out, they fell into an age-old trap of producing a sequel with the original movie's main star written out. It has never worked at the box office. Even the original Alien series was built around a star, Weaver, not around faceless, voiceless xenos who the general audience has no emotional connection to.
They should've instead had Shaw and David's derelict ship crash on a moon in the vicinity of the Engineers' world that turns out to house a xeno science lab, staffed by a small number of Engineers who could be dispensed of quickly in the beginning. They discover that the Engineers have kidnapped other humans and humanoids and are experimenting on them. There could even be a Walter android among them to keep the dual role angle for Fassbender, because the Engineers were exploring synthetic reproductive possibilities as well.
Shaw and David then find where other people are locked away in a cell and move to save them, but then David betrays her, deciding he wants to continue the experiments, and Shaw is trapped. Then the rest of the movie is Shaw and the other humans trying to escape their dungeon and get off the moon while David attacks them with his xeno creations. There could be a time lapse here even of years while David works on his science projects and bumps the humans off one by one before they get an escape opportunity. And we could still find out that David creates the classic xeno in the end. But the key is that, like Ripley, Shaw survives in the end.
This also avoids retreading the LONG opening Covenant section of yet another new and oblivious space crew landing on a foreign world, finding crashed derelict ships and getting infected with aliens. We did not need to see that yet again.