Prometheus was barely an Alien movie. Scott saying it has "Alien DNA" was just a lose term for having a few minor references and connections. Prometheus probably didn't even start out as an Alien movie, you could change the ship design around slightly for the Engineers, Replace the Engineers with some Random E.Ts and Boom!, you got a run of the mill Sci-fi movie about some Black Goo DNA changing shit.
It's Barely.... An Alien movie.
You have some valid ideas, however, Prometheus did start as an Alien movie — as evinced by the early script drafts. This is not to take away from some of the film's faults, which are augmented quite ironically, by the BTS and supplemental materials released.
As of late, comments like those made by NickisSmart and others make me nervous for Covenant because the film took such a long time, scriptwise, to come together. With 17 actors billed so far, I have doubts about how effective an ensemble cast of this size can be given the the delays in production. I want to be hyped for this film, I really enjoyed Prometheus, and what we have seen thus far looks promising and mysterious (in a more direct and less obtuse way than in Prometheus). I just want to be able to invest myself more in the characters this time around.