Why do all of Ridley's protagonists have to be stupid?

Rating: 5/10 (1 June 2017)

As in Prometheus, the plot in this movie can't advance without one of the protagonists being completely incompetent or stupid.
In Prometheus the SME (subject matter expert) is always bad at what the one thing they are supposed to do well. E.g. The biologist/zoologist touches strange living worm and gets bitten. The navigation and mapping expert gets lost. You get the idea.
In this movie the leader is incapable of making decisions. The soldiers/security team suck at providing security, panic in the middle of combat. The pilot can't fly straight. Everyone wanders off alone immediately after being attacked by hostile alien organisms. No one asks straight questions when they are huge elephants in the room: holy sh*t, there is an ancient city full of cadavers here!? Who built the city? Are they still here? Are they a threat? Do they have radios we can use? How about space ships or weapons? No, instead they mope about their poor decisions and wander off one at a time to be killed.
My point being is that it sucks that for the plot to advance, the protagonist has to be incompetent or stupid. Not only is this implausible (NASA picks the absolute best candidates for space missions, people that won't panic or make stupid decisions) but unnecessary. I really don't think it's so hard to setup a challenge in the plot where the protagonists suffer at challenges despite giving it their best. In Aliens (Alien 2), the space marine company enters in the facility and gets ambushed by aliens. Despite their firepower and blasting the crap out of every alien they see, they still get overwhelmed and take casualties. They didn't all need to stumble around, trip and fall into a pit in order to get in trouble; the aliens laid a trap and overwhelmed them. In Alien the crew of the Nostromo gave it their damnedest and still got taken out one by one.
Upside to the movie: I like the way they brought the over-arching plot of the aliens to completion, explaining the variation in the different types.
Still they left more questions unanswered: In Prometheus, after a spacecraft leaves the planet an Engineer kills himself and then dissolves into Earth's water giving way to life. At the end of the movie Elizabeth Shaw heads to the Engineer home planet to find out why they are hostile towards humans.
Why did the Engineer kill himself on Earth in Prometheus thereby "seeding" the planet? Was the seeding done intentionally?
Did the Engineers ever return to the habitable planet where they just left an Engineer who dissolved into the water and discover the human civilization that grew from his seed?
If the "seeding" of Earth with Engineer intentional then why did the Engineers never bother to communicate with their creation?
How did early human civilizations get the "star maps" that lead the Prometheus to a LV-223?
Why is the Engineer on LV-223 in Prometheus hostile towards humans?
Are all the Engineers hostile towards humans?
Why did the Engineers create the weaponized virus that becomes the aliens? Why did the Engineers store the weaponized virus on a LV-223 in unsecured and fragile containers?
Why was there a video of Engineers running away from aliens on LV-223?
Why did the Engineers never send a recovery team to LV-223 to recover the Engineers who died in the installation?
Why did the Engineers allow a long lost and potentially rogue ship to return to their home planet without first being screened by any sort of security (given the potential for weaponized viruses at least a bio-scan/quarantine procedure should be in place for an advanced space faring civilization)?
Were no Engineers off-planet or in a spaceship when David released the weaponized virus on their home planet?
Why are all of the Engineers located only on one city on their planet?
One of the Engineers in David's lair was flayed, not destroyed by the virus. Did some of the
Engineers survive the initial attack?
If some Engineers survived the initial attack, how was David able to defeat the them?
Why did the advanced-space faring Engineers not have any satellites or space stations in orbit?
Why did Covenant crew only pick up Elizabeth Shaw's lingering transmission and no lingering transmissions from any of the Engineers who lived on the planet?
Why was there wheat on the Engineers' planet?
Did Elizabeth plant the wheat before she was killed by David, did she have seeds? Or does this mean that Engineers visited Earth and brought it back? Or does this mean that the Engineers visited Earth and bestowed wheat on the humans, only later wanting to destroy them and creating a weaponized virus to do so?
Why was Walter removing a sole embryo in the beginning of the movie? Was he conducting his own side experiments?
Why did the Covenant crew not have access to the same or better technology than the Prometheus crew (e.g. the geo-mapping drones, dune buggies, and space suits)?
If Mother and Walter(David) could track the alien through the ship and funnel it by opening and closing doors why confront it at all?
Why not just funnel it to an airlock and blow it into space without sacrificing heavy industrial equipment that will be needed for the future colony?