The Death: While Daniels (Katherine Waterston) explores David's (Michael Fassbender) lab, she comes across the dissected, mutilated corpse of Prometheus survivor Elizabeth Shaw (Noomi Rapace), who David had clearly been performing grotesque experiments upon.
Who Should've Died Instead: As solid as Katherine Waterston was in this movie, it would've been much more interesting to see Daniels killed off in the third act by David, at which point a surviving Shaw would become the surprise protagonist for the final showdown against the Xenomorphs.
Considering that Prometheus got fans invested in Shaw's journey to the Engineer planet, her off-screen death felt like Ridley Scott flipping a giant middle-finger at them.
Had Shaw instead taken Daniels' third-act role, her being fooled by David in the final scene would be easier to believe (her having had minimal contact with Walter and all).
Plus, if Shaw had an actual role, the movie may not have bombed at the box office, which effectively killed any prospect of a direct sequel featuring Daniels or indeed anyone. The idea of Shaw rather than Daniels going into stasis with a nefarious David controlling the wheel would've been a much cooler setup for Covenant's sequel.