Why did it take so long for Daniels to figure out Walter was actually David?
OK, despite the fact that I clearly have a pathological need to stand up for this movie against claims that it doesn't make any sense, I can't defend the final twist. Why does Daniels, clearly the smartest person on this crew, trust the robot she thinks is Walter? Yes, David cut off his own hand to appear more like Walter, but she should have done a more thorough test. Hasn't she seen a horror movie before? Also, why did Walter help Daniels and Tennessee in their final fight against the alien aboard the Covenant? Why not let them die? Cut all ties.
Also, on a narrative-level, it's such a clearly telegraphed twist that it makes the ending, where David waltzes away with some alien embryos, predictable. The grandeur of it all, the Wagner thundering away on the soundtrack, has an unearned quality. It fills you with dread, but there's an absurdity to it as well.
Then again, this wouldn't be a 21st Century Alien film directed by Ridley Scott if there weren't something to shake your head about as you leave the theater. More than the mythology, that ability to terrify and confound in equal measure might be this prequel's greatest innovation.