Just saw it again today. I liked it even more than before. I still put my ranking as Aliens, Alien, and then Covenant. I still don't like the pacing of the third act, it still seems rushed. I really hope we get a director's cut on blu-ray. 15-20 more minutes, with the majority of that added in the third act, would really elevate this film I feel. The third act needs a little more tension, a little more cat and mouse with the beast.
It seems like there were a good amount of people who didn't like Prometheus. but eventually they liked it. I'm not saying everyone who dislikes Covenant will end up liking it. However, I think Covenant is a movie that people will like the more they watch it. Just my opinion.
Also, I thought of something while watching it today about no breathing masks or protection for when they landed. Once they determine to check out the new planet, we are told the trip will take 2 weeks. The repairs on the ship only need 48 hours. I would say it's implied that all the tests to make sure the new destination is safe for exploration would have been carried out in the 12 days after the repairs have been made. Again, just my opinion.