I really can't see how Prometheus is better than even the studio mangled theatrical cut of Alien 3, let alone the extended one.
Both have pretty cringe worthy dialogue and some flaky characters but the prisoners are prisoners, not the hand picked crew of a quadzillionaire's scientific research vessel.
Both have atmosphere and a strong central performance but for me at least Alien 3 is much better.
It was obviously not the same bone ship but I think that a lot of people have been fooled into thinking it's the same ship because of it's history of once being the same ship in the original UAP script.