How can Prometheus have been set in the same Alien world at all. The technology shown was totally different to the other films which were set after it.
If you are going to do a prequel then rule number 1 is get the continuity correct.
The other aliens films were largely set in places where the money wouldn't have been spent on "best" tech or nice looking tech, but the best value for money or utilitarian technology that did the job.
From memory it's mentioned in Alien that the ship needed an overhaul/had a backlog of problems that needed fixed which would suggest it was an old ship (rather like a tramp steamer), also the company wasn't going to send a brand new ship on a mission that could result in it's loss (not only for cost reasons, than it's harder to explain what it was doing there).
The tech in Aliens was better cared for but again utilitarian and varied depending on if it was Earth Station (relatively nice, clean, modern), the Marine ship (clean but very utilitarian), or the ground base (very utilitarian).
Whilst the ship in Promethious was a brand new(?) ship equipped with state of the art technology such as the auto doc as used by the head of the company.
You even see the same sort of thing with the space suits, the ones on the Nostromo were obviously well worn, older design that were intended to be worn by people on a daily basis doing dirty/possibly dangerous work (such as maintenance in space), whilst the ones on the Promethium where more advanced/newer and intended for use by the likes of Scientists (as fitted the ship being an exploration one, rather than a basically a space truck).
The extended universe books do a bit of playing around with the background of the Human factions and expands on the idea (as shown in the films) that the Company is basically only giving out the good tech where it's needed and saving every penny it can at the expense of people's lives on the front line.
For example one of the books set a fairly long time after Aliens* mentions that they had one of the "new" autodoc units on a mining ship, not because the company cared for the miners, but because it was cheaper and led to less downtime (so more profit), whilst the one in Promethium was (from memory) mentioned as being a very expensive item and I think as a prototype or one of only a handful made.
Also from what I remember of the film and the books, there is a strong suggestion that the Engineers may have been fighting another alien race, or been involved in some form of civil war (hence the proto Aliens as a weapon).
The Alien books "Out of the Shadows", "Sea of Sorrows" and "River of pain" are pretty good reads and tie into the various gaps between the films, from memory "Out of the shadows" is set between Alien and Aliens, "Sea of Sorrows" is set just before Aliens on LV-426 (and expands on the bits shown in the Directors cut of Aliens).
*It features Ripley's Great Grandson I think.