The other two scenes they cut which I thought could've been added (with some work) were when Fifield and Milburn find the familiar shedded alien skin and a few large worms he puts into metal containers.
There was also the Shaw VS Engineer scene, which I have mixed feelings about.
I remember reading a comment by, I think Ridley scott on why it was removed (that a weakened shaw was able to fend off the engineer), but still, seeing him entering the lifeboat, gently examining the crystal chandelier with his hands and reaching out to the big movie screen with the girl playing the violin, shon a different light on the engineer.
There was also a photo of him crouched down, looking at the contents of a book.
They should've somehow added those scenes back in and removed some of the ones I found pointless, like the awkward scene between Vickers and the captain and him asking if she was a robot, I would've much rather seen the engineer speaking, than that pointless scene.