I thought it was Whedon who wrote the film as a parody (or at least, so he claims...); it was everyone else who played the script straight and obscured the whole comedy angle. At any rate, I refuse to give a pass to a movie whose intended meaning can only be derived by looking up what the creator(s) later said about it because the movie itself failed to communicate a consistent or coherent tone. A work of art must be able to stand on its own, full-stop.
Still, you can always count on Jim to bring up good points even when you disagree with his overall argument. The chief example in this case is the Newborn, which I also quite liked in spite of my instincts screaming at me that I shouldn't. In its five minutes of screentime, it conveyed a more diverse range of emotions than the entire rest of the film. The practical effects work in general is great, particularly the xenomorph costumes, and even some of the CG stuff looks good (like the laser-activated glass of beer). Plus, Sigourney Weaver's performance, nicely distinct from those she gave in the previous movies in fitting with the significantly altered version of Ripley, once again elevates the material surrounding her, especially in the scenes where she first meets Winona Ryder's character and comes across the lab full of failed clones.