Prometheus is the worst of the six because, interesting as it is conceptually and as nice looking as it is, it really has no excuse for being such a structural mess (both at the script level and, inexplicably, even worse in the edit). I don't hate Prometheus by any means (the ideas at its core really do work for me, even when the execution never really lives up to them), but also, I can't make excuses for it/forgive it for its warts quite the way I can with Alien 3, given that one's notably messy production.
Covenant rocks.