Lindelof: "The movie asks the question, were we created by these beings? And it answers that question very definitively. But in the wake of that answer there's a new question, which is, they created us but now they want to destroy us, why did they change their minds? That's the question that Shaw is asking at the end of this movie, the one that she wants answered."

My problem with this thinking is that they pretty much answered that question with the very first scene. Then the next two hours were watching a group of 17 (4 of whom were actually invested at all with this question) trying to catch up with us so they could ask a new question.

Also, the matter of fertility that he mentions earlier in the interview was almost completely random in this one. The entire "I can't have a baby" moment was unnecessary. Ripley lost a child and it gave her extra motivation to look after Newt. Shaw couldn't have a baby and when she found out she was pregnant... she immediately wanted it out of her anyway.

And that's the problem here, almost nothing matters. There are countless scenes, like the fertility moment, that could be lost without changing anything.
On top of that, nobody has any sort of arc. Charlize's character should have been the one to survive; gone from not believing to wanting to finish the job. And flamethrowing that dude could have been played as her doing the right thing even if people didn't think it was humane. Although how, after they'd already seen an infected Engineer head explode, anyone thought letting dude on board was a good idea was beyond me. I mean, the lack of protocol on that ship was astonishing.
(Meanwhile, Shaw actually does a kind of 360 - wanting to go, wanting to leave, to wanting to go to the next planet.)
Half of the stuff we learn about people doesn't matter, like when the guy who doesn't want friends stays by the cowardly biologist who inexplicably plays with an alien snake (mind you, moments after seeing the hologram of beings three times his size running in fear and then found piled up dead. It doesn't take a scientist to know that the one remaining living being might not be friendly.)

Again, it was like Lindelof worked off of an outline and had to stick to that outline regardless of how little sense things made and then ended up with this mess of a script. Asking big questions is fine but when, in doing so, you create a ton of little questions for which you have no explanation, you've done it wrong.