Well Im a big, big fan of Alien 3 so I wouldnt change much in it, I would only corrected some mytho mistakes and plotholes but other than that Id leave everything intact. It wouldve been better and more humane to have just Ripley eject from the ship, but on the other hand the movie would loose the strong emotional punch and there wouldnt be anything to trigger Ripley's metamorphosis into a masculine, emotionally burned out person.
Just leave the autopsy out of the movie. That would be my only request. Its just sick and really unhealthy. I would never want to see , even in a movie, an autopsy on a child. There are limits