The real issue is... Prometheus doesn't really know what it is and where it is going. While it's still a moderately entertaining movie that can be enjoyed on some levels, it's a shame to see the wasted potential. Story-wise it was incoherent, the writers simply didn't focus on the job.
It must have been written with LV-426 in mind, since it used all the classic imagery from Alien. Changing the location to LV-223 is probably the most egregious example of sloppy writing in the movie.
Erich von Däniken's theories make an interesting movie premise. Is it really so hard to execute it in an interesting manner? Writers of the Stargate franchise had an uninterrupted run of 14 years and they didn't explore the premise very well (they just preferred to play it safe and focus on the action & humor).
Most of the bad science doesn't really bother me - I guess at this point I've gotten used to it. Remember the supernova that "threatened to destroy the galaxy" in Star Trek (2009)? It was way worse than anything in Prometheus... And we've seen FTL travel and artificial gravity in all other Alien movies (we simply didn't know the exact date). It's just very hard to portray interstellar travel without them.