Alien and Aliens don't exist in a vacuum. In the next 30 years the franchise gave us the underperforming and (unfairly) maligned Alien 3, the underperforming and pretty much terrible Resurrection, a sub-par Paul W.S. Anderson B-movie and one of the worst pieces of shit slasher movies ever.
Alien is a tainted brand with a shrinking fan base. Fox's previous administration got that and distanced Prometheus from Alien. The new regime got cocky (and stupid listening to fanboys) and went back to the poisoned well for Covenant.
By the way, Prometheus was well-reviewed and liked in the real world.