The biggest problem with Prometheus is a lack of unified vision.
Prometheus was supposed to be one of the best films ever. Everything about it indicated that it would be a new classic of modern filmmaking: A talented director, with a great reputation for compelling science fiction films, a cast full of young and skilled actors, and a gigantic budget to allow for production values that skyrocket.
When the film hit the theaters though, there was nothing of substance to be found. The film was great visually, that effects budget was surely not wasted, but pretty much everything else about the film was painfully bad. This series of four articles looks into what could have been done to make the film work for a discerning sci-fi audience. Of course, expect lots of spoilers.
Last week we learned part of the reason for this problem was competing visions for the film. The studio wanted a new property, the beginning of a franchise unconnected to director Ridley Scott's previous work, but Scott wanted to make the Alien prequel that he had originally signed on for. This accounts for the mixed up plot that made the film seem like it was a slip-shod mess with no real arc.
The easiest solution to fix a lot of what was wrong with Prometheus then would have been to solidify that original vision, to make sure that the director was on board with making the film that the studio wanted him to make, or to get the studio to let the famed director make the movie he wanted. Either one would have been better than what hit theaters: a film in which two plots compete for your attention, neither of which get a proper resolution, yet create a cast of characters with unfathomable motivations.
What would that film have looked like?
If Scott had been allowed to follow his original vision: The pods of magic black ink the characters found on the Engineer's ship would have been Xenomorph eggs instead, and the scientist who were attacked early in the film would have been attacked by a face-hugger instead of a mysterious ink-snake for which no origin is explained or even hinted at. Holloway would also have been a face-hugger victim, instead of being ink-duped. David's motivations would have been a little clearer, as there would have been something more tangible for him to study.
It would have been clear from the get-go that the Engineers had made the Xenomorphs, and that they had made them as weapons. The discovery that the cargo was originally targeted for Earth would have had a stronger impact on the audience, who already know how devastating these creatures could be, and the relationship between the Engineers and the humans would have been clarified and solidified.
Further, there would have been no reason for the questionable evolutionary process that the Ink/Xenomorph takes over the course of the film, although, that means we likely would also have lost one of the most visually and emotionally intense scenes of the film, the med-pod sequence - not that it really belonged anymore anyhow. In general, the film would have been clearer and more interesting to the fans of the Alien universe, which is pretty much the entire potential audience for the film.
If Scott had acceded to the studio's desire for a non-Alien film: It's harder to see exactly what would have happened here, since that plan wasn't laid out for us, and a lot of new things would have been invented, but with the Xenomorph connection removed, the film would have been cleared to explore other possible types of alien life, adding more mystery, and more hard scientific interest to the film.
Also, as above, there would have been no reason for the questionable evolutionary process that the Ink/Xenomorph takes over the course of the film; It could have evolved instead into some other more sensical creature, or even had some other effect. Acting more like a rapid mutation agent, for example, would have made more sense, and allowed for more possibilities for freighting 'human' monsters like the one that the geologist became.
This still leaves a lot of issues with the development of the characters, and errors in the ways they were used, but I'll address those in parts 3 and 4 of Repairing Prometheus. First I want to discuss the science of the film. Look for that in Part 2.