The real problem with a prequel is how to get humans in there.
If the suits had a problem with a wooden planet full of space monks I doubt if they would put money into a 2 hr movie with just Giger's designs wiggling about on a bone ship.
These issues are discussed rather well in this article :
http://www.denofgeek.com/movies/259949/the_plotobstacles_to_an_alien_prequel.html
I don't have the same problem about the Company knowing that the ship is there and sending the Nostromo out to investigate with Ash onboard as the author of the article has.
Burke in Aliens wasn't very high up in the chain of command and sent the colonists out to the co-ordinates in Ripley's report to feather his own nest so clearly information is passed around on a need to know basis, with in house rivals tending to their own pet projects.
Perhaps there was a previous encounter which someone in the Company wanted to capitalise on and sent the Nostromo out in the same way that Burke does 57 years later.
If this was a personal project of a Company stooge when the ship vanished the perpetrator may have covered his or her failiure up not knowing that Ripley was still floating out there waiting to awake company interest again almost six decades down the line.
I quite like the idea suggested by O'Bannon that the eggs were the remains of a civilised race and the Jockey's crew woke them without adults to provide the education necessary to turn them into anything more than very dangerous feral children.
My better half maintains that the space jokey was a cosmic pizza delivery boy and that the eggs were a strange delicacy from a very dangerous world were the xenomorphs are relatively harmless compared to the other nightmarish creatures that keep their numbers in check .