There are a lot of scenes we have not seen in the deleted scenes, there are reasons they was cut and you can i you look at all the shots in the link above work out indeed there was another version of the movie, that got cut and edited and re-aranged that led to why the movie we got had some pacing problems.
If we accepted a movie that had for instance the Weyland in Cargo Hold as Fifield was attacking and then shown was Shaw who ran him over this would maybe add a more smooth pace to the movie.
With a keen eye you can spot that some scenes was re-done and the re-done scenes made it to the cut and not the Orginal ones...
The Last Battle Scene, especially... you see as the Trilobite and Engineer fight, we see the Engineer has a disapearing and reapearing Burn Mark....
The deleted scenes and ones not shown i.e Engineer leaving his seat and running across the LV 223 surface to get to the lifeboat, these add some depth to the movie and give us clues that allow us to chalk off some explanations.. for example the what happened to the Engineers Mask as he entered the lifeboat... how did he survive outside etc...
The not shown scenes prove that he never needed it....
The deleted scenes i.e longer battle one shows us the Engineer also as well as the scene above did not have a burn but also lends more depth to the Engineer along with the full Engineer Speaks Scene..
Ultimately what we got shown as the Engineer simply did not like us, and wanted us dead and after his ship crashed he got burnt and then wanted to go and kill off Shaw...
This and the deleting of the Elders shows me Ridley wants to portray these Engineers as a ruthless race who have no concern or care for Mankind... which then Begs the why create us and visit us and teach us in the first place question...
Simple as the cut we got, well could be one of the worst you could make if you had every footage at your disposal.
