Alien 3 was a production hell. Writers/storys and directors changed during the production. The 3d graphic engine wasn't good enough for this type of movie production. At the end, the 3d alien model looked shity. It looked like a B movie. Surely David Fincher was a first time movie director, lack of moive production experience, but he can't take all the blame for the failure of the movie. A few years later, he end up finished some great movies such as Seven and Fight Club.
I think most of the problem are coming from 20th century fox. Look at both AVP moives, they are just destroying the 'Alien' band. Same go to Terminator 3, and Xmen 3. The 'company' control the 'creativity'.