I think the Problems all come from how they tackle a Prequel...
Lets look at the Franchise, we arrive at the Nostromo being rerouted to check out a Signal, they discover a Alien Ship, with a Alien Pilot, who's Ship has a Alien Cargo. A crew member is infected with the Cargo, which we can assume was the fate of the Pilot too.
The sequel set 50+ years latter, we discover the WY Company have set up a Colony on the same Moon that the Nostromo had discovered the Alien Parasite, the company loses contact with the colony and Ripley is told about it and off we go, we discover some Colonist explored the Derelict and brought the Parasite to the Colony which then over took the Colony. And at the end the Humans win again with Ripley surviving and seeing the Colony Blown up by a Nuclear Explosion.
Then we get the 3rd movie, the Survivors on the Sulaco are ejected out due to a Fire and land on a near by Prison Planet, only Ripley Survives, a Face Hugger infects a Animal and one gets on the loose as the Prisoners and Ripley Fight for Survival, before finding out Ripley is infected with a Queen Xenomorph, the company arrive and wish to take Ripley back but she knows there plans and Kills herself.
I will skip AR because this is where the Franchise suffered, but the idea is the same as the others, The COMPANY wishes to gain and exploit the Xenomorph Parasite and Ripley comes to the Rescue.
In each movie, their is the Agenda of the Company and its Wishes for the Xenomorph and the Great Lengths in disregard for Human Life to Obtain this FOLLY
When tackling a Prequel... maybe this Agenda and what leads to Special Order 937 is something that could have been explored.
The other thing was NO-ONE had ever shown us the Xenomorphs Origin, HOW/WHEN and WHERE was it created, WHY/WHEN did the Space Jockey have the Egg Cargo and WHERE was he going with it and WHAT was the Purpose
So began the Prequels.... during the stages they decided its just as important to cover who the SPACE JOCKEY was, we have seen the Xenomorph over and over including the AVP movies but NO-ONE covered the Space Jockey.
So a Plan was made a Plot, a Bold and Ambitious one which uncovered the Engineers being a Ancient Humanoid Race who Partake in Genetic Engineering and how they had Engineered Mankind, a Plot that brought with it Philosophical and Religious/Mythical Questions about Creation. Maybe ERROR in Hindsight? But it certainly opened doors, and also allowed for the History of Weyland and AI to be connected to these Philosophical ideas.
But what role was the Xenomorph? a Engineered Bio-Weapon created to Eradicate Wayward Creation, and so the Evolution of Alien Engineers to Prometheus was to conclude that the Xenomorph was a Bi-Product or even Origin to the Engineers Evil Biological Warfare... The Xenomorph/Black Goo to the Engineers is no more than Nuclear Revolution that leads to Atomic Warfare or discovery of Gunpowder that leaves to the Evolution of various Weapons of Warfare.
The Question was not so much WHAT the Xenomorph was but WHY and WHY was it created and so Prometheus left us mild hints via connection to LV-223 the Black Goo but the MAIN point was the WHY
But Fans did not like Prometheus in masses so FOX felt, and seeing Blomkamps Alien 5 getting a interest they felt they had to Answer or start to Answer the events that lead from LV-223 to the Derelict on LV-426, while showing us HOW the Xenomorph was created, and WHEN and WHERE Themes that RS felt did not need to be answered in Prometheus and that bigger things could be explored as they moved away from Alien, while leaving those clues for us to try and connect those dots ( Which RS then commented on and GAVE the Space Jockey Answer).
But having FOX cave in and wish to ANSWER the WHEN/WHERE/HOW and lead up to the Back Door of Alien, and bringing the Xenomorph back in and actually now moving towards Alien as opposed to away.
It appears RS, wanted to throw a Curveball to the THING that he always wanted to explore, which was the WHY only in doing so, he felt that David being the Creator would be a interesting Curve-ball and thus would follow on the Philosophy of Creator, creates, Creation Rebels and Sub-creates and the Hubris of the Engineers Creating Mankind, and Failing to Eradicate us before their Fears would come true... indeed there Fears did come true... and our Folly for trying to Mimic the Gods and Create David provided also to be our Hubris and so REVEAL David had Created IT.
This Logically has to now follow that Davids Creation either Turns on Him and gets out of Control, or those above the Engineers witness Davids Creation and look on in high regard for Davids Achievements and seek to take Davids Creation to Engineer themselves. Either way providing to be their Downfall.
The Company then in the Franchise, choose to Pursue this Folly but always Failing... we have to ask WHY? and i think a reveal Curveball regarding AI's role in terms of who is pulling the strings would have been that Answer.