Alien 3 really is a flawed gem. The production woes on the picure are well documented, so the fact that Fincher manged to pull through is a testament to the guys talent.
I agree with Wookster in that's it got some of the best acting in the series, especiallly Weaver, Dance and Dutton. The "I must make you nervous" scene still sends shivers down my spine. The Alien's birth scene (Dog version), the Attack on Dance and the "kiss", when Ripley finds out she is impregnated, there's so many good scenes that firmly outweigh the bad.
Also ADI's FX are really good in the film which makes me wonder why they kept dropping the ball in the subsequent Ressurection and AVP movies. The Alien looks superb and the mangled Bishop was way ahead of it's time in execution.
Plus it's just so darned Nihilistic and devastated the audience from the very beginning with the death of Hicks and Newt. Which is a very brave thing to do when you think about it.
The bad? The majority of the prisoners are ill defined (go to to love Morse though). The full Alien shots are mainly not that hot. There are some pacing issues and a few clunky lines of dialog.
Thinking about it the film is probably more of a character piece than the other films and that's no bad thing. I think that when it was released the "fans" were hoping for a kick ass action film and got a dark, grim, art film effectively. One that was neutered by the removal of the Golic scenes, rendering it confused in it's narrative.
Hopefully one day Fincher will forget the pain of the shoot and revisit the film to re-cut it to the masterpiece that it truly could be.
In summary It's a love it for me.