The original idea for the movie was for Newt (the child from Aliens) to be cloned, not Ripley. This was changed when Sigourney Weaver agreed to reprise her role.
Weaver was impressed with Whedon’s script. She thought that the error during Ripley’s cloning process would allow her to further explore the character, since Ripley becoming part human and part alien would create uncertainty about where her loyalties lay. This was an interesting concept to Weaver, who thought the film brought back the spirit of Alien and Aliens. She was reportedly paid $11 million (more than the cost of the entire first Alien film).
The underwater sequence marked the first time that Winona Ryder had gone underwater since a near-drowning incident that happened to her when she was 12 years old. The actress suffered a complete anxiety attack on the first day of filming in the underwater set. imdb