Haven't looked at the medpod scene properly yet but had a look at the rough ending - it's still quite a mess.
A big issue with including the deleted / alternate scenes at the end there is that there are a lot of incomplete visual effects - composites of David's head / shaw in a harness / CG scarring missing from the Engineer...
- you might be able to hide a lot of this by darkening footage on these two sets [life pod / juggernaut control room]
it might be difficult but more interesting to only show the Engineer [in the life pod] in the dark / from a distance / only show his legs while the focus is on Shaw hiding...
- the colour grading also varies between shots.
Personally, i wouldn't spend so much time showing the demise of the Engineer when we wont see him again.
another big problem is it paints Shaw as a main character which is something you've been trying to avoid.
IMO, this absolutely has to go -
DAVID - ...He's coming for you!
SHAW - Who...Who's coming?
???
Who else could it possibly be?
The focus should be on David trying to manipulate Shaw into helping him leave the planet.
David - Does it matter why they changed their minds?
Shaw - Yes. Yes it does
David - Why?
Shaw - because Fuck you that's why!
I also really don't like the alternate version of Shaw stuffing David's head into the bag - it really feels like an outtake.
I did have a similar idea about moving the opening sequence to the end but it kinda feels weird - music is good though! - Unless you could imply that what we are seeing is the place that Shaw and David are intending to go to..
maybe a dramatic pullback to reveal an unfamiliar galaxy? or two suns in the sky or something..