This script completely removes or explains all the weird character decisions and plot holes, opting instead for badass one-liners ("I brought it in. [hefts her gun] I took it out"). Engineers has a new take on the chest-burster scene that's even more intense than the one Prometheus gave us: Instead of getting a cesarean section, the original draft had that medical pod repairing Watt's chest as a xenomorph burst out of it. We also would've seen new types of xenomorphs, including a gray human-alien hybrid -- except, ya know, better than the one we saw in Alien: Resurrection.
And no one has sex with it!
Weirdly enough, it also explains virtually every plot hole in the version we saw. Why does the crew not know what their job is? Because classified jobs pay more and Peter Weyland is worried about corporate espionage. What's the black goo? A bioweapon originally intended for Earth. Why does the Engineer throw a temper tantrum when people wake him up? Because he has a xenomorph in his belly and is awaiting medical care -- our heroes have effectively doomed both him and the planet. Why did David the Android turn evil? Because he goes nuts and starts seeing the Engineers as gods worthy of worship.
So what happened? Well, they brought in Damon Lindelof (the guy who wrote Lost) and, shockingly, suddenly the plot took on the same random and nonsensical nature of the seasons of Lost he wrote. Lindelof convinced director Ridley Scott that the movie didn't need to be an Alien prequel at all, that audiences wouldn't care about that. So instead they'd just make the aliens look pretty much like the xenomorphs everyone knows and loves and do a "search and replace" in the script, switching out the names of the planets. After all, there's nothing audiences love more than being utterly confused by random plot elements that seem to have been slapped together on the fly, right?