I still think a lot of it had to do with the marketing. Fox seems to still think they've made a horror movie, which is not the case. Aside from that, I agree that the current zeitgeist doesn't lend itself well to films like Covenant. I honestly don't think its going to get any better. Superhero movies and other big budget CGI-fests are here to stay.
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Eventually they will lose traction too. The Marvel/DC cinematic universes appeal to the public today in the same way that westerns appealed to the world for decades. None of these things are forever.