Prometheus is more of a thematically cohesive film, whereas alien is a bit scattershot in it's ideas, it's brilliantly done but its hard to drill down to find more than just a slasher film in space.
Prometheus is just drenched in symbolism and meaning, most of which is present in showing the different ways in which we are motivated and driven as humans. The hired scientists represent greed, Vickers represents resentment, Weyland is obviously trying to cheat death. David is the zen one, going along simply because that is the way things are, and Then there is Shaw, who is motivated but simple genuine curiosity and love of discovery, She is motivated by just wanting to learn more, instead of just a particular outcome.
Just rattling off the top of my head...