Prometheus has so much potential to be better, which is what makes it so frustrating for me. Great visuals, sound and some themes are interesting - there is a legendary sci-fi defining film under here somewhere... The film as a whole, however, feels segmented and like a plethora of different people's input scattered about with no fruition to any of it. Characters are odd and not how people talk or behave. The plot is also weird; and under scrutiny makes no sense. And I think the Engineers were uninspired.
Covenant, while still having odd characters and ones that aren't fleshed out, tends to feel more focused at least. It's also a much darker tone which I feel is more in line with the Alien series. An aspect that I really enjoy about it, too, is that it's almost like a self-contained little horror piece. Apart from all that, though, the usual Ridley Scott visual awesomeness is here, as well as much better music and atmosphere.