As I've posted before it seems as if it started out as a pretty solid Alien prequel script (face huggers, eggs, chestbursters etc) and then the suits wobbled.
Possibly out of fear of other prequels of note not fairing well or possibly because if the toys were the same they wouldn't sell enough toys (Alien junk sells, even I got plastic crap from both of the AVP films and I loathed the second one).
Ergo the announcement of this not being in anyway a prequel just a story set in the same universe.
Then they twitched again and worried that if they had no links with Alien the pre-existing fanbase wouldn't plug in to their dream/toy machine and bolted back on Alien bits in a haphazard way.
I just hope they bring out a really good Space Jockey and gun thing (the boneship would be cool too) so I can pretend it's from Alien and not from Prometheus.
Just look at Ridley's own Robin Hood, the script was thought of a masterpiece (the good King John holding back the vile terrorist Robin) then the suits twitched and it became a vehicle for Russell Crowe's global accent.
I also think it was constructed with PG13 in mind but they didn't count on the classification board getting the jitters over the medpod scene.
Hardly any of the violence is bloody (even David doesn't squirt much of the white stuff).