I just watched Prometheus again with the Lindelof/Spaights commentary. Lindelof admits he is pretentious about 15 times throughout the commentary. Apparently the commentary track was recorded before Prometheus' release, but somehow he knew that people would hate it. He spends most of the commentary trying to explain the scenes that don't make any sense. Most of the time his explanation is "we wanted to add more mystery" or something along the lines of "I changed it because I'm pretentious, sorry if you don't like it". Some stuff did make more sense after understanding where Lindelof and Scott where coming from, but it just didn't come across after deleting so many scenes and changing around the Spaights script. Almost everything interesting in the movie was originally thought up by Spaights and he seems very down to earth about it all. A couple times you could hear him cringe at the changes they made, but both writers give kudos to each other.
To answer your questions as I understand them after listening to what Lindelof had to say:
Why were the engineers in the security hologram running? - because they weren't able to contain the goo, there was an outbreak it it created some kind of monster - You don't see the monster in the hologram because "we wanted it to be more mysterious".
Why would they run to the room with the black goo? - Understanding that there is a complex tunnel system, there was probably another exit in that room somewhere. Or, they just panic'd, or it was bad writing.
What the f%&* is the black goo really used for. Creation or destruction? - Creation, but what it creates depends on . . . "well, we want that to remain mysterious"
Did they create us, were we an accident? - Yes, they created us, but apparently they weren't happy with the results. "why? we wanted to keep it mysterious"
Why 2000 years into hyper sleep did he want to kill us and return to earth and kill everyone there? - I think the plan was to dump black goo on us about 2000 years ago, but due to the outbreak killing all the engineers, they weren't able to complete the task. Perhaps the last engineer was in hypersleep before the outbreak took place, we will never know, "it's a mystery"
Why was there an Alien on the wall in the one room, but never around until the end when a mutant face hugging baby created one? - there is no acceptable answer for this IMO, just bad writing.
Why did David feel the need to kill people for no reason? - they kind of touched on this in the commentary, multiple reasons, none of which came across very clearly. Lindelof said David was under-impressed with his creators, but he was also carrying out orders to do whatever it takes to get the answers to immortality for Weyland. I don't think he knew what exactly would happen to Holloway when he gave him the goo, but maybe it would give him some answers for Weyland. Also, they wanted to keep David's motivations mysterious.
There are 1001 more unanswered questions I have about the movie that would all be answered with "we wanted to keep it mysterious" from Lindelof.
