Well, they say kill your darlings, right?
I think that Vincent Ward and David Fincher weren't really thinking about Alien3 in terms of being the stewards of a franchise (After all, apart from maybe Bond and Star Trek, these sprawling franchises with ten or more movies and a streaming series on the side just didn't exist back then. Star Wars was a franchise, yes, but it was still only three movies. Okay, five, if you want to count the wacky stuff). They just wanted to make that one movie. And I think that used to be a strength of the franchise - that it didn't really behave like a franchise. Each of the first three entries had its own artistic integrity. They didn't want to set up a sequel, keeping all characters that might be needed available. They wanted to tell a story. And Alien 3 had no qualms about nuking the previous movie from orbit to do that. And I really respect that.