That's an interesting observation. I'd venture it's because Alien 3 is the first of the "bad ones." The franchise was phenomenal until that point, so expectations were higher than they've ever been since. Well, that and it's the one that kills Newt and Hicks.
I believe Alien 3 would have been a very interesting limited TV series. Obviously in the early 90's, the SFX, structure, logistics and format just didn't support something like that, not at the kind of visual level expected of the Alien franchise.
You have a lot of characters, and they all look alike ( shaved heads, wearing rags, middle aged white guys, etc, etc) Then it's dark. And it's nihilist. That's just too much to dump on an audience in a couple of hours. I don't see Alien 3 as as bad story, just an abbreviated one given the circumstances. Give this 13 hours, a limited "prestige" TV series, with a lot of character development plus decent homage to Newt and Hicks and then you might have something really special. If you have more time to develop more of the prisoner characters, you have a better chance to help the audience feel the total loss and hopelessness. Also flashbacks to the Sulaco would allow a proper send off to Hicks and Newt, or a story workaround, that honors them and organically removes them from the prison storyline. It would also help to create some merchandising potential and spin offs as well.
Charles Dance, Charles Dutton and Ralph Brown all had interesting characters. Just not fleshed out. A TV series could explore why they are there and why it matters to save the hopeless.
Some stories just don't fit the format it's given. Enders Game is an incredible story. Maybe one of the best modern science fiction novels ever written. However you can't fit that into a single movie. You'd need multiple season of high level prestige television to even begin to do it justice.
Alien 3, from a narrative standpoint, was only going to work if it centered around Newt. In order for the sacrifice of so many lives to save her ( remember the Aliens mission was effectively a rescue mission as well) to mean something, her life itself had to have critical importance against the looming threat of a future alien invasion. Ripley dying makes perfect sense. If it complements Newt transitioning from child to adult. Much how the alien gestates through it's life cycle in something different.
It's pretty sad for fans though, because Weaver is actually a tremendous actress in the most natural sense. If not for her insatiable ego and narcissism, this series could have really broken some new ground in what was possible for science fiction films. Alas, she had to be Patty Jenkins before there was a Patty Jenkins.