Let's agree to ignore the awful VS Predator crossovers for a second. I'm not sure they are canon anyway, and they are obviously cash grabs and not made with the same care of even the worst Alien movies.
Alien 3, while it has a cool idea (prison planet), is a mess as a result of executive meddling (the story can be read online). And they killed Hicks and Newt... bastards!
Resurrection was awful and awfully badly acted. I like Jeunet, but this was a hard miss. It has some cool visuals at times, typical of Jeunet, but the movie itself was embarrassing.
Prometheus was atrocious. Badly acted, badly scripted (characters making the dumbest of choices at every turn, professionals who don't know their profession -- xenobiologists who pet alien snakes, geologists who get lots at the first turn -- this has been discussed countless times). And the loss of mystery... nobody needed to know more about the Engineers/Pilot aliens, that's not how good storytelling works. Aided by technology, Scott "pulled a George Lucas" and forgot the cardinal rule of scifi horror/mystery: less is more.
After this, I exercised the good sense of avoiding Covenant (the plot summary seems bad), and Romulus, and now the new TV show.
I think overall the gravest sin is that the Alien universe was meant to be sketched in the broadest strokes, and details and mystery kept, not overexplained.
I wish they had let the first two awesome movies rest in peace.
Extended universes suck.
P.S. same applies to Blade Runner. Then again, I didn't even like the sequel, so I'm sure I'll dislike the upcoming show :(