1. The squid in the lab grew so large, because it grows fast. It grew from one cell, to that "baby" size in a day.

2. I asssumed that they wanted to destroy Earth because it was a possible threat. That's why the engineer freaked when he saw humans woke him up. I think that David did try to be friends with the engineer. He was programmed by Weyland and was there to figure out how to help Weyland live longer. The story did not indicate that David gained human emotion. But when he explained that they were humans from Earth, the engineer wasn't happy.

3. Problems caused by David were at the whim of Weyland, who had only days to live after he woke. Weyland was reckless and thought he'd find a way to lengthen his life.

4. Guy Pierce put on the makeup because there is a deleted scene with a younger Weyland.

5. Black stem cell goo + engineer = xenomorph (doesn't matter which engineer it is). Just like mealworms + goo = snake things.

6. The hyroglyphics never said that the engineers wanted to be found or meet up with humans. They were just hyroglyphics, indicating that star map. For all we know, primitive humans kicked some alien ass thousands of years ago and the aliens ran, in hopes of developing the stem cell goo and destroying humans.

So the way I saw the movie (this is more for me than you)...

1. Engineers land and work on planet. They use the planet as a "remote test site" for the black stem cell goo. The engineer in the begining would have been the one who started the growing process. It sacrificed itself so the other engineers could harvest the black goo for a long time, in mass quantites (I don't think it had anything to do with terraforming).

2. During their work there, the black stem cell goo gets out of control and kills everything. We saw the dead engineers. But we don't know what killed them. It could have been the mealworms + black goo = snake things. Or any other living organism that the black goo attached itself to. You know, we only saw a square mile of the planet. There could have been some Chutulu sonofabitch on the other side. Or maybe some xenomorphs had already developed (and ran, and lived/died elsewhere on the planet).

3. 2000 years later, the crew find them on that planet. They're pointed there through the hyroglyphics. But the hyroglyphics never said, "hey, these guys want to meet you".

4. They explore and wake up the one engineer. Engineer is not happy about humans finding him. Humans are viewed as a threat. Even if they weren't in the threatening position that David and Weyland created, humans still would have found the engineer.

5. Awakened engineer tries to carry on the plan of destroying Earth (you'd think we'd have Earth defenses anyways in a time of lighspeed travel, whatever). The badass captain stops that plan. Everyone dies. Except lady and robot, who are off in space with an insurmountable amount of stem cell goo that could kill everyone on the engineer's planet. And turn the whole planet into Xenomorphs. Unless they're really shooting for something else, I think that's where the sequel would go.

Really, the only thing that made me suspend disbelief was when the just tore that squid out of her womb. They way she just tore the cord out felt silly. They go through all of that effort to create some sort of real world (this wasn't Men in Black), and then they couldn't tighten up that scene a little?