A few thoughts/questions:
1. If the engineers were human, why were they ~3ft. taller than the actual humans?
2. If the planet/moon was an outpost for the engineers to build bio WMDs on, then why did they put an invitation to humans on Earth to come visit there instead of their homeworld?
3. What pissed the engineers off?
4. What were the little snake/cobra thingys?
5. Did the Aliens originate from a parasite? i.e. Big things in small packages?
6. What was the point behind David fucking everything up? I realize he was directly working for Weyland, but I still see no reason to sabotage everything.
7. What caused ol' boy with the tats on his head to come back to life? Let alone, as some fucked up, super strong creature thing.