Prometheus could never have been a good film... No way.
Alien is among "the greats" in horror/science fiction cinema. A substantial part of that was involving H.R. Giger in the Alien design and "biomechanics." Giger was a (albeit heroin-addicted) genius.
Aliens, however, is also among the strangest of movie sequels because the film was a genre flip from horror (that happened to also be science fiction) to an action/adventure film (that also happened to be science fiction). The "egg-laying" mother alien, was never part of the H.R. Giger Alien design, but it certainly worked within the confines of the movie. Giger had arranged an entire life-cycle to the Alien. Yes, you can look it up or even find it in his published etchings/artwork. There was a cut scene from the movie (that you can probably find it online somewhere) that showed Dallas being consumed and turned into an "egg." It was felt that it was one more terrible horror in a film that already had just the right amount of scares and gore.
Ret-conning the Alien biology and attempting to force-fit it into a larger framework was one of the MANY flaws that doomed Prometheus. Aliens showed you didn't have to stay true to an internal mythology to make a great film. Even if that internal mythology was extensive. Why Prometheus tried to re-do that still makes zero sense. There was no need...
The other issue that is completely unforgivable in Prometheus is the complete lack of science throughout the film. Let's not be safe or even remotely scientific in (just about) every decision we make in the movie (from checking the atmosphere before attempting to breathe it, etc). You don't have to be a scientist to make a good science fiction movie. Plus, you can use unexplainable non-scientific things (Star Trek does ALL THE TIME) like transporters and warp speed and Time Travel and genesis devices (and have a jolly good time at the movies). You CANNOT, however, be consistently, unfathomably stupid and still have a good science-fiction movie. Unless, of course, that is your goal. Then go for it-- No one minds when you do stupid well (eg,. "Bill and Ted's Excellent Adventure," "Harold and Kumar go to White Castle," etc).
Prometheus was an abhorrence in film-making, story-telling, myth/world-building, etc. It failed on every conceivable level.
You don't need to go back to "Alien" DNA to make a good new Alien story. You just cannot be as moronic as Prometheus. Hell, I'd be willing to bet that AI could generate a half-decent Alien story with just a few prompts. It takes real human beings to fail at the level that Promethues does.