Both Prometheus and Covenant had good ideas, but the final product was lacking and a bit of all over the place. The main issue, for me, was linking them to the Alien universe. They messed everything up, had too many retcons and the timeline doesn't make sense. If they had gone with a new sci-fi franchise, completely removed from Alien, about the origin of humankind, playing God, etc. it could have been great, Scott always delivers visually and there's a lot of interesting ideas...but as part of the Alien universe they're pretty weak.
That sums up my own feelings quite well. I loved that the newer movies were ambitious and tried to tackle the big ideas of classic science fiction and philosophy. Do we have a creator? If so, why did He/She/They create us? What obligations do we have to them -- or to those that we ourselves create? Is it even wise to create A.I. or explore a potentially hostile universe? Those are all valid questions, and it is great to explore them in fiction. Yet, I consider these movies flawed because they didn't pay enough attention to the details of how it all matches up with the continuity of the ALIEN universe, and many of the human characters are not handled well -- almost like the humans were an afterthought. The humans in these movies are supposed to be highly educated with scientists among them yet don't even take basic precautions which is so annoying to watch. Ridley Scott's visuals and David Fassbender's performances make them worth watching, and I still consider them good movies -- but seriously flawed on the script-writing and world-building side. It was like they had a lot of grand ideas but lacked a rigorous editor challenging them to have everything make sense and fit together in a logical way. PROMETHEUS should have focused on the creator/human/android dynamic, which deserved its own movie. ALIEN: COVENANT should have been a follow up to that with a focus on the creators, or engineers, and why they created us and why they wanted to destroy us -- and could still have included them being brought low by their thematic "grandchild" David. It would have been interesting if perhaps they wanted to create us to serve but once they found out we had developed technology that could threaten them (i.e. throw them down the way the Olympian gods threw down the titans) that was why they wanted to destroy us. If David found a way to destroy them, in a way that would make them right.
In my mind, the retcon of David creating the Xenomorphs simply isn't true. Yes, he tampered with DNA and created something, perhaps similar to the Xenomorph, but like Walter told David he was flawed ("Who wrote OZYMANDIUS?" "Byron." "Shelley. When one note is off it eventually destroys the whole symphony, David."). David may have believed he was this great creator, but he was only playing at being God and tampering with things beyond his understanding. Whatever the Xenomorphs are is still shrouded in mystery. They've been around long enough for a Space Jockey that had a chestburster erupt out of it to become fossilized, which means over 10,000 years. My idea is to have a mixture of the various sources. In the Dark Horse comics, the Xenomorphs evolved from a particular ecosystem, a harsh planet which could even produce variants like we saw with the Black and Red Xenomorphs. Sometime later, however, a higher species like the Engineers tampered with or modified the Xenomorphs to make them even more dangerous, and perhaps even biomechanical in the sense of being silicon-based and having metal teeth and able to digest metal and minerals and having a rapidly increased metabolism far beyond anything nature alone could evolve. This was probably also tied into the religion of the Engineers which was obsessed with perfection and sacrifice. The Xenomorphs were developed into the perfect weapon, but one that was perhaps too perfect, as they are ultimately uncontrollable... It is the classic theme of hubris that seems to run through the ALIEN movies.
You could say the same theme is reflected with the synthetic persons we create to serve yet who at times turn against us or prove uncontrollable.
Janek's sacrifice in PROMETHEUS, along with the other crew members, could be that which made us worthy to survive -- which calls us back to the sacrifice of the young engineer at the beginning of the movie.