I've been giving this a bit more thought recently.

I would have had the dissolution scene, cut straight to the ship, have the Isle Of Skye scene play as Holloway's dream, have Shaw's phone call to Weyland play as Vickers' dream that way you'd have three dreams which would be about Shaw and her relationship to the crew.

I would have showed the TED talk instead of Lawrence Of Arabia on David's 'home cinema'.

I would have cut the briefing, cut the need to pretend that Weyland is dead and have Fifield and Milburn attacked when they all went inside the head chamber the first time.

In the trailers we see the same 'chalice' from the beginning in the position of the mysterious green jewel. I'd put that back.

Lose the bringing back of the engineer's head.

Have the urn the only artifact retrieved.

That way we learn that the Jockey head is a space suit mask when it is lowered over the engineer.

I'd have the Fifield Mutant and Holloway killed in the same scene and have Shaw in the medpod when David and Weyland have their chat with the engineer.

She could be ejected inside it before the crash cutting from the birth scene straight to the fight for survival (no giant squid fight just a modified face hugger on the engineer would be enough).

Shaw makes no assumptions about the engineers changing their minds about us.

This makes their actions totally inscrutable and alien.

It might make for a very short film though.