I hope those extra twenty minutes is where they kept all of the characterization, or explained why "Checkov's" self-surgery pod existed and was only programmed for a man when it was in Theron's personal quarters. If it was for Weyland, why? She wanted him dead, no surgery could have saved him from anything anyway.

But seriously, most of the characters were just there. And not like a cheesy horror movie where they each had their cliche, they were just there. The captain of the Prometheus didn't seem phased by any of his crew dying, and ended up ramming the Space Jockey ship with volunteers I'm pretty sure had no dialog until that point. "Alien" managed to make you care about each character, even making you guess at who the main character is. "Prometheus" gives you the main character, who barely acts human, does things because they're symbolic, and is surrounded by people whose names we don't even remember.

By the way, I loved catching the first Sunday showing at my local theater. The wife and I were the only people in there, so we could talk like we would at home. "I'm sure that Theron's quarters are a life support pod will never enter into this again", mostly just "come on!"