Covenant as a film is better structured and has better pacing than Prometheus, bar the last rushed act. But if they ever decide to do a new Prometheus cut, trimming down a lot of it, specially the dumb stuff which is very easy to take from the movie (as it's been done in many fan cuts) and including some of the deleted scenes, maybe my opinion would change.
Both the things I like and dislike in both are very different from one another, so they almost balance each other out. But as a movie, Covenant is more solid.