When you really break it down that doesn't hold up as strongly as first impression may give though.

The ship is not the same ship as Alien. The Engineer is not the same creature seen in Alien--that creature has a slightly different face, slightly different design and is still about 20% larger. It's also attached to the chair, as in the designs overlap, not just growing onto it from decay. That one also carries alien eggs, never seen in Prometheus. The planet is different. None of the characters are the same--except the Weyland namesake. Even the state of technology seems to be on a different timeline (yes, I relaize it's because in the 1970s that's how it seemed things would go). Plus, the styles of the two films are quie different, other than having sci-fi/horror elements.

But you are right, the design and the set-pieces definitely recall Alien and are clearly intentionally based around the designs from that film.

That's why I say it isn't really isn't a prequel. It's a film that takes the design elements and set-pieces from Alien and re-configures them for a story that is apart. At the most one could say it runs parallel. It's not really a sequel, but yet it's not distinctive enough to be truely seen as it's own thing, so it's that rare category of pseudo-sequel. There are a few historical precedents that have been made similarly, and they have always confused audiences as well. But prequel? That seems too definitive a term. I guess Prometheus 2 could easily turn the tables and tie it in with the Alien series better. But from what Scott has said, Prometheus 2 will be even more disconnected and take the series on it's own unique trajectory that almost completely leaves behind the Alien origins of the storyline. I think if that happens--and it seems to be in motion--people will be able to better frame the series as a parallel or alternate-universe sort of series, which I think will help.