Oh yeah so my opinion for the topic is that it's not a good prequel for Alien, but in theory (because I dislike the film, irrelevant) works better as another story in the same universe. Little ties Prometheus directly to the events in Alien so it's not really a set-up story for Alien.
Biggest difference would be the tech as others have mentioned before. But for those who really care about continuity it can be somewhat justified (classic 'really old blue collar tug vs billions of dollars top of the line exploration vehicle' argument), as can the discrepancies with the space jockeys (different tech, one out of the two ships we've seen is older/different from the other).