I like Covenant way better. Its tone, its atmosphere, its themes. I love the nihilism, the AI aspects and the Frankenstein nature of it. Even right down to the music is superb. Covenant can also be viewed as a singular entry, which is sort of how I view it. To me, it doesn't really fit with Prometheus despite its links because it's so sharply tonally different, and it doesn't quite fit with the Alien series either (IMO), but by itself it's such a great film and a great side story.
I hope they get to make another one, but I'm hoping they fill in more about the Engineers, because I don't think they should just be swept to the side like they seem to have been at the moment.