Ironically, I think the future films in the franchise may have helped Alien 3 by expanding the Alien myths beyond Ripley and not letting this be the "end".I love a franchise film that clearly despises franchises.
When it came out, for me at least, it really burned all of its goodwill away in the first few minutes due to killing off Newt and Hicks - undercutting the relatively happy, yet earned, ending of Aliens. Naturally the whole film stays that dark so I understand the point, but it is an example where I think it is a mistake in any sequel to undermine the emotional beats of the prior film so that the hero's effort was essentially for nothing. To me it almost didn't matter how good (or not) the rest of the film was after that decision.