It's not a very smart film,
What exactly was smart about "Alien"? It had a very basic and straight forward story but what made "Alien" a classic was how visceral and creative that simple story was told. And of course HR Giger's amazing artistry.
I do agree with you though on your point about "Prometheus" having some logical gaps but you'll find logic gaps in pretty much any sci-fi film if you analyze it closely enough.
The logic gaps in this film were HUGE though. Big narrative holes/continuity errors.
We're not talking light sabers...which you just have to not think about at all.
Alien was a different kind of movie, so such a critique doesn't apply. It's clear that Scott was trying for something
completely different with Prometheus, and clearly missed the mark.
That's me being nit picky though - I actually enjoyed myself while watching the movie.