Ridley Scott has said that the DVD will contain (either as deleted scenes or a longer cut) up to 20 minutes of footage that didn't make it into the theatrical cut. I would suggest that the problems with odd motivations and strange story jumps might be explained in the longer format.
That's how I saw it. There is a theory that within the Engineer race, there are the creators (wearing hoods) and the warriors (wearing the body armour) and they potentially are on different sides when it comes to seeding life on planets such as earth (something we may see in any sequel?)
I can't remember exactly which they were, but the friends I went with well vouch that for me, there were two very obvious jump out of my skin moments.
. Still think it is a genius movie.
Oddly, the more I think about the film the better I regard it. As long as people don't expect a direct prequel to Alien, and understand this is not set on the same planet as Alien, it's a great, visually outstanding movie. I might go and see it again this weekend.
I've had a few hours to mull it over and I think it's brilliant. It's definitely not alien 2, but within it's own storyline it's very good. On IMAX 3d it was incredible and the 3d was very immersive. Sets up the sequel nicely.