The movie made sense IMO, its main issues are that so much of the crew are hollow. Their characters are threadbare, they're on screen for the express purpose of dying. Even if we don't pick up on it specifically we pick up on it subconsciously and they feel off. The geologist and biologist that die early on have basically one trait each (biologist is fake tough guy, biologist is nerdy-nervous). They don't feel like real people.

I liked Prometheus a lot, but the very-real problems with it would in my estimation require way more than a director's cut to fix. Unless there's a lot of filmed character development out there, I suppose. The insignificant characters needed to be replaced with a far smaller number of significant characters to join the handful of existing significant characters. Basically requires a rewrite.