It really depends on what version of Prometheus we're talking about, and who was in charge at the time.
If we're talking about Ridley Scott's vision and not scripts that came along the way, it was even less Alien-related and more Engineer / Synthetic related. That survived in the final film in a kind of malformed manner by relating the human-engineer relationship to the synthetic-human relation... created an creator. The Alien stuff was somewhat forced in by the studio. and the "Deacon" at the end of Prometheus was meant to be his new interpretation of the Xenomorph. Prometheus originally had a much looser connection to the Alien franchise. Calling it a spiritual reboot wouldn't be too far off. Ridley Scott created Alien 40 years ago, and it had been through so many different hands, that by the time he came back to it with Prometheus, he wanted to just disconnect it from all the additions of the sequels, AVP and so forth. He just had no interest in Alien queens, dog aliens and all that stuff. Prometheus' alien was the mutagenic spore.
Prometheus did well, but Fox felt it could have done better. So when Prometheus 2 was greenlighted, it was instructed to pull it into a closer direction with the franchise. Noomi Rapace was supposed to return and find the Engineer's homeworld. Instead that became a kind of mini-prequel to Alien Covenant and we got a very different movie instead, one that featured an authentic xenomorph and alien eggs (again, with some differences), but also more of the stuff Ridley Scott really cares about - the mutagenic spore, and androids. The franchise Xenomorph stuff? Scott still isn't all that interested in it. His original vision of Prometheus 2, again, had lots of engineers and nothing with the Xenomorph.
He still wants to do a third, but his problem is that he has less interest in things involving the Xenomorph and lots of interest in the rogue AI and creator/created stuff that the David plot is all about.
This is, Disney, which now owns Alien, probably isn't about that at all.
Alien Covenant wasn't a failure. But it wasn't exactly a success either. It made over twice its budget, but it didn't do the business Fox hoped a more Alien-centric sequel to Prometheus would do. It made a lot less money than Prometheus. A lot of that is probably on the studio, that didn't really get behind the movie and market it. It got eaten alive by Guardians of the Galaxy 2.
Disney will likely want to go back to basics, and go big, when they decide to push a major new Alien production. Probably a new director a very studio-run creative process like the Marvel movies. And probably a much more aggressive marketing push that differentiates the next film as "Disney's Alien 1" rather than "Alien 7". That way they can try and make a billion-dollar film out of it. Heck, they're already showing up in Marvel Comics.