Here's a sketchy idea that would likely sell:
PROMETHEUS 2 takes place b/w ALIEN and ALIENS - as Lindeloff stated (something I always thought would work actually) - making the PROMETHEUS films run parallel to the ALIEN films, or better yet, as midquels to them.
It's 10 years after ALIEN and Shaw's 39 year old son who barely remembers his mother delves deep into the corporate conspiracy he believes is responsible for covering up his mother's disappearance. This is all triggered after finding all kinds of files about her theories in his late teens.
So then, he joins WEYLAND CORP - NOW, rechristened 'WEYLAND-YUTANI' and weaves his way into a position as some sort of case manager where he can access date files on company employees.
That's how and when he finds information about another possible cover-up - the events on board the Nostromo - and (HERE'S THE CLINCHER) he reaches out to someone else he believes may be in a similar situation - AMANDA RIPLEY McCLAREN and possibly her father, as well. Together they team up and either a) Combat the Company in a film with very little Alien or Engineer content or B) Stowaway on some sort of follow-up mission to LV-223 or LV-426 or better yet, some other planetoid in the Zeta-Reticuli system that reveals another component of just what the Engineers were up to there.
Eventually, it turns out that AMANDA RIPLEY MCCLAREN was killed by the company to 'silence' her knowledge.
You know, I wrote this thinking it was bad, but the more I consider what we might ACTUALLY get, this doesn't sound that terrible. I mean, I know if my parents dissapeared in space during some shady operation, I would certainly investigate for years if need be and it adds a relatable human angle PROMETHEUS lacked. Plus, putting off finding out what happened to SHAW and DAVID,...might add mystery.
You know what, this is just making it all too clear to me that I don't really care to see what happens to those two. Maybe its just me, but some things are better left unsaid and I think keeping what the Engineers are up to, a secret is probably better than explaining it.