This is one huge spoiler so stop reading if you have not seen the movie.
Elizabeth Shaw flies off into the sunset? Really?
My wife and I saw Prometheus yesterday and walked away both thinking the same thing. The tension peaked when they returned to the ship with a sick Halloway and it went down hill after that. So over some lunch we talked about how to make it better.
A character we loved but felt was flat and under utilized was Theron's. Why not build on the tension between Vickers, David and their father. Vickers was a 'company man' - always doing what was right for by the company and always hoping to impress her father. This plays into the strong "evil company" theme familiar to Alien and Aliens. Theron was already skeptical / jealous of David and her father's plans so why not make this a central theme. Why not see Vickers go from "company man" to realizing she is nothing but a pawn for a bat shit crazy old man.
After the scene were David tells Shaw she is pregnant jump to Vicker and David confronting each other again. This time Vickers learns David purposely infected Halloway and the news of Shaw along with David's plans to bring her back to Earth.
Instead of the timid Shaw over powering two people and performing an operation on herself we see Vickers save her (I won't even mention how dumb it is that Meridith Vickers has a male only operating robot on her private escape pod). This would be much more believable than the mousy Shaw going rambo and its starts showing Vickers change of allegiance while still remaining a strong character.
Now her confrontation with her father is even more powerful and can really flesh out her bitterness and realization that he has only ever cared about himself above even mankind. We also agreed it was stupid to use Guy Pearce in this roll but always show him in makeup. The intro video should have been of the real Guy Pearce. I mean, if you can do a hologram letter you can surely give yourself a face lift in it. It would make seeing the 'old' Guy Pearce that much creeper.
Now skip to Shaw running back to the Prometheus as the derelict ship takes off. When Vickers sees all this she has an epiphany realizing her action have probably ended the human race. She is in agreement to crash the derelict ship but the captain, being a gentleman, forces Vickers into the escape pod.
With both females on the planet running from the crashing derelict ship we reverse the rolls. Nobody cares about Shaw anyway plus it's a prequel so nobody is expecting anyone to live. Shaw gets crushed and the audience smirks...which is more of a reaction than you get killing off Vickers who suddenly turned into a running scared mouse. Instead, by keeping Vickers alive and strong at the end you can do two things better.
You can have an actual believable and epic fight between Vickers and the space jockey (with Vickers prevailing in a similar manner since that is the setup). A real boss fight would be much better than the anti-climactic crashing of the space ship and a mousy Shaw going toe to toe with the space jockey.
Secondly, when the fight is over David can deliver his same lines to Vickers. How much more powerful is this now that it is his "sister". Vickers enters the derelict to retrieve David....or does she. She is carrying the flame thrower and torches David to a crisp while delivering some witty line, "I'd rather die alone on this rock".