Few changes I remember off the top of my head:
1) Opening is a little different, originally you didn't see Franco's corpse and them cleaning up the colonist pods.
2) Slightly longer scene where Daniels mourns Franco.
3) Shaw prologue is in the film, it begins when David talks to Walter with his flashback (before bombing)
4)
Spoiler
I don't remember seeing Shaw's corpse in the original cut, but I could be wrong.
5) David/Walter switch is much less telegraphed and more subtle
6) Ending is completely different, top to bottom.
That's what I remember being the most different, apart from that there might have been alternate angles etc.