Bad writing and ideas will do that. Taking something that should be simple, and creating some large philosophical diatribe out of it isn't always the best thing to do. I personally call it, "The Nolan Effect". The beast itself is far from dead, Alien Isolation, unused movie scripts and several of the novels are proof of that. I'm of the personal belief that the narrative needs to move in a different direction immediately; even if it means not finishing the trilogy on film. Let David and his ship become the Space Titanic, (though obviously somewhat different) the mystery ship with thousands of people who fell victim to an accident and vanished into the dark depths of space.
Regardless, It's not the beasts fault. The Prometheus storyline has never really been about the Xenomorph, and when they were used, they were used exceptionally poorly. It's just my opinion, but what's needed now is an "Aliens " type movie. See if Cameron will come back, he's talked about doing another terminator for heaven's sake. Do something with action and alittle spectacle to draw in the younger crowd and therefore the money. Establish new interest and a financial base to take off from. When the choice is transformers or Alien Covenant, people are going to see the explosions and gunfire, not Shakespeare on Mars. An Alien queen being blasted by a colonial Marine will attract more attention than David in his "Little white Onesie". The Alien universe can handle a good action movie, look at the second film, or better yet, Gibson's Alien 3 script. Or just do like the saw movies, repeated formula (minus any connection to any other film). Random crew on random ship or base encounters an Alien or Aliens and fights to survive. Smaller budget with a consistent offering, and give different people the opportunity to direct each one.
Either way, I don't think it's the beast that's "cooked" or "run out", but I'm starting to think Ridley is. If he has no faith in, or passion for the beast, he shouldn't be directing the films they're in.