So here's what I'm guessing at.
"Alien" was a nifty little horror film that dealt with interconnected themes of rape/corporate abuse/robotics/insect life. "Aliens" was a completely different vision from a completely different director, so forget about that one. "Prometheus" will form the true third part of a trilogy, but will be much bigger in scope than the original. Alas, the same director is around, so the rape/corporate abuse/robotics/insect life will return, but this time in full throttle. If you choose to see this film, prepare to question the meaning of life and walk away with a bad taste in your mouth. A horror film is not supposed to scare you. A thriller does that. A horror film is supposed to horrify you, to disturb and bother you.
So here's an outline as to my predictions for the film. I use a mixture of facts gleaned from the last few months and my own conjecture.
1) Humans discover star map. They go to planet. Duh. No one fan is disputing this.
2) They arrive on planet (not the one from "Alien"). There they find a derelict spacecraft. They go inside, where they discover all manner of bizarre, almost mechanically biological life (setting the groundwork again for Scott's interconnecting themes of rape/corporate abuse/robotics/insect life, but expect it to be more tortuously painful and disturbing to watch).
3) Some of this life attack one of the humans.
4) The human (with mohawk?) begins to change at the biological level. Maybe it's a symbiotic/parasitic arrangement? He begins to turn into a Space Jockey (there, I said it... everyone else seems to just take it for granted that Space Jockeys are completely different and have no connection to humans. I contend that the "Engineers" ARE human, somehow at least).
5) The human/Space Jockey starts to attack others. The crew of the Prometheus realize that the threat is not only to them, but to all of human kind. The Space Jockey is like a dark, monstrous version of the Star Child from "2001: A Space Odyssey," and those egg-like cylinders that have confused us all are like monoliths, but tangibly filled with icky DNA-altering goo.
6) The Space Jockey fixes/builds the spacecraft to go to Earth. The Prometheus crew realize that if it gets there, all of human kind will be ruined, that the whole purpose of human existence is to be converted/serve as hosts for these Space Jockeys.
7) The Prometheus pursues across space.
8) While in transit, the robot David figures out a way to alter the genome sequence and create something that will destroy the Space Jockeys, e.i. turn the weapon against them. A xenomorph essentially, except that that term is Cameron's name and not Scott's.
9) They catch up to the ship and stop it, losing all their own people while they're at it. Rapace's character succeeds in stopping the Jockeys, but in the meantime becomes infected herself. She turns into THE Jockey we all know and feel sorry for, the one from the first "Alien."
10) The xenomorphs (Scott will never call them that) make there way into the picture. And the nasty kicker of the film, the twist ending: the Gods have ANTICIPATED the humans creating the xenomorphs. The Gods KNOW that this is the way it will play out. The whole point is not to populate a new planet with Space Jockeys, but to provoke the humans into MAKING SOMETHING WORSE. That's the heartless raping/corporate/robotic/insect-like horror at the heart of the matter.
Because the Gods are NOT the Jockeys. The Gods either never appear (making them more intimidating and the story more Lovecraftian) or are the shapeless-yet-squirming primordial goo. Life is nothing more than efficient organic robotics. There is no higher purpose. We're mold on a piece of crust, mere atoms and molecules, like David or Ash. The life cycle goes like this: life is seeded on a planet. Life evolves and goes searching for meaning. Life destroys itself. The Gods are shapeless monsters. Lovecraft is exalted once more.
Anyway, that's my thinking. Let me know how you feel about it.