I'd say that Prometheus isn't a good movie. I like it, I find it fascinating conceptually, it's very nice looking... but it's also an absolute mess at both the script level and in its final edit, and it doesn't have any excuses for being like that the way that Alien 3 does.
I wouldn't trade Prometheus in, I'm happy that it exists and I remain endlessly intrigued by it, but it's the one out of six in the series that I am unable to bring myself to actually call good. Thankfully, it coasts by on interesting, which is a lot more than the worst movie of most franchises can claim.
Unless we count the AVPs as part of the Alien series, then the worst movies of the lot are both bad AND uninteresting...
