Jean-Pierre Jeunet is very much an auteur. He only makes Jean-Pierre Jeunet films, much like Tim Burton only makes Tim Burton films. The problem is that Jeunet, like Burton, has a very warped sensibility that's completely wrong for an Alien movie, and he gives the proceedings a generally absurd feel, especially when it comes to the scientists and military. And thus the general described as "ramrod straight and about as gruff as you would expect" in a scene like this
CUT TO: INT. PEREZ'S QUARTERS CONTINUOUS
He is mostly dressed, still shaking off sleep. He stands at the command console,
bringing up visual. Everything on the screens is smoke and noise.
comes out like this in the movie:
That's not an imposing general about to deal with a crisis concerning a lethal Alien species, it's the school janitor suffering through another prank by some pesky kids. Quite possibly one involving bananas and buckets of urine. It's an endless litany of scenes that are played completely wrong. Turning Gediman, the one sympathetic scientist into a freak that likes to make faces at the Aliens in their pens. Making Vriess a comic relief character mugging for the camera. Casting Winona Ryder. Having the hybrid look ridiculous and make out with Ripley.
Which is not to say that Whedon's script is perfect in every way, especially since Alien is still my favourite and this is more a rollicking action-adventure starring a gang of cool outsiders, Whedon's favourite pony doing its favourite trick again. The cloning stuff is the same hokey nonsense, for starters. (Although to be fair, it's not like there were a lot of ways to bring back Ripley, and given that "Alien 3 was all just a dream" was considered for a while, it could have been so much worse.) But it's pretty solid, features recognizable human beings, has a suitably epic showdown on earth, and the hybrid does not make out with Ripley.
That last point, I feel, is pretty important.