Welcome to the forum. Very good topic and ideas. It is likely a sequel to Covenant would be have a scenario akin to what you describe in your point # 1. Even though I find your second and third scenarios  to be much more interesting, the need of connecting to the first Alien make it more difficult to go in that direction. However, those themes can still appear in the story, which would be awesome. I think many of the ideas members of the forum have been coming up with have the the potential of providing the basis for very good movies, not necessarily connected to the Alien universe. The idea of a higher intelligence communicating with its creation through a coded language (maybe through dna design?) would be fascinating.

The only problem that I see with introducing new ideas is the wasted potential we have witnessed in previous installments. It is like you introduce a character or a storyline or a theme that didn't stick with the audience in a way that you have liked, and instead of trying to fix them or to develop them, you just kill them so you don't have to deal with them in the future. That is why we don't have Elizabeth Shaw, Engineers or a quest for "where we come from". I think the new movie needs a change of angle, a re-evaluation of the David character, and further exploration of themes introduced by "Prometheus".

Good story ideas.

I'm a little concerned they don't have access to the Giger art style. Might not be able to follow through on his work.

I wonder if Weyland-Yutani had to keep ash's android identity a secret because of the fallout from David? Can't have the Nostromo crew worried about our synth....just say he's human..have him hyper sleep...eat with them....gain their trust.    So maybe the Nostromo had heard of David?

Who inside the Space Jockey would be the biggest shock for everyone?

Should they even try to bridge the Space Jockey? Or just leave it as is...a thousand year old pilot.

What would be satisfying conclusion to the final prequel.....?

The death of David? 

Find out who was the Space Jockey?

Giger's Biomechanical(copyright issues) coming to life/death?

Star Wars prequels felt like they flowed really well into the next episode(s). Is it possible? A smooth transition from Alien prequels to A L I E N?

I don't think the identity of the Space Jockey need to be shocking. The important part of it is to reveal the "why, when and how". It just cannot be David.

A satisfying conclusion of the prequels would be to finally know what is at stake for humanity in their face off with the Engineers.

If Alien Covenant was the last installment or if you strictly follow what we have learnt in AC in the last prequel, then the post Aliens movies would have very few elements to work storywise. That is why the Engineers and their mythology need to remain in the game for the sequels. And it was a mistake to declare that the "beast is cooked"; that is the same as making Dracula movies convinced that the vampire is finished.

Welcome Pym of Nantucket great thread and ideas!!! Thanks for sharing your thoughts.