I have no idea what Scott or his writers are doing with these movies and I don't think they do either.
i will use this phrase as the premise to my opinion; obviously you understand that what follows is speculation, as none of us can look inside Scott's mind.
Alien 1 is a film based on mystery; where did the aliens come from ? where does the ship come from? who were they? None of these questions are answered in Alien 1, and they don't need to be - all you need to know is that the crew needs to GTFO from the Nostromo.
In Alien 2 the same happens again; i mean, really, it's the same.exact.plot as Alien 1 - eggs from the same exact ship infect humans. And again the humans need to do some hardcore GTFO.
Alien 3 did not try to make a mystery of any of that, whether by the camerawork, by the expressions of the actors, by the dialogue, on the contrary; "there's an alien? we need to make sure that there's no ALIEN. A this tall this wide here-is-a-mugshot alien that does THIS to people. oh look, THERE IS THE ALIEN, DOING THIS TO PEOPLE".
Again Alien 4 did not try to put any mystery into the film.
Both Promoetheus and Covenant tried to feed the nerd frenzy of the fanboys and tried to "answer the questions". Who are the engineers, what are the aliens, what is the relationship between the two. And i think the black goo was added to add a further layer of mystery to the film.
Now, the problem lies in trying to explain a mystery. First off, there is no indication that the mystery was to be solved at all.
I'm gonna move sideways for a second and reminisce on how good the Mass Effect 1 story is, because Sheppard is fighting against an enemy that cannot be defeated; we don't care, we love that she makes a heroic stand, and we don't fully see the enemy, only know of it as an obscure presence.
When later they humanize theenemy into something that can be - and is - defeated, it looses that sense of impending doom which is the main appeal of her story. (i played as a chick, ok? sue me)
If you want to write a good Alien-series film, you not only don't need to explain the mysteries at the core of the series, you shouldn't need to. Unfortunately, nerds make a lot of noise and more than one franchise (*Star Wars*) has been ruined by their own communities, because the writers will try to appease that vocal minority that looooooves double-bladed lightsabers but fuck the mainstream viewer.
In Prometheus, the main culprits are on one hand the stupid behaviour of everyone involved, with the "oh look at this poor fella, he looks just like A DEADLY COBRA FROM EARTH, i will fucking pet it", but also that the rest of the film is concerned with trying to lay out as plainly as possible the nature of the engineers, the aliens, the goo, leaving nothing to the imagination. And it chooses to replace suspense with action.
We .. back in the days of Alien 1 .. were better than this. Sure, the facehugger looks cool, but what made the film good is two characters looking at this thing around a crewman's neck, and the exchange: "what is this thing?" A: "we don't know".
Not "it's a stage 2 quadrupetal endoparasitoid Xenomorph XX121 of the Enternecivus Raptus species from LV-416".
I didn't make this ship up. It's on Wikipedia, official, canon shit that came from offscreen fanboy work. You can't make films this way.