The film had an infamously troubled production, with reports of clashes between director Frank Oz and stars Nicole Kidman and Bette Midler. In later interviews, Kidman, Matthew Broderick, and producer Scott Rudin all expressed regret for being part of this movie. Kidman reportedly almost left the project, dissatisfied with the script rewrites. Oz has reported regrets over his involvement, admitting that he feels he made too many mistakes, cared too much about what the studios, audiences, and producers wanted, and ultimately delivered a substandard project.
Heavily re-edited and re-written following test screenings, with new scenes shot and others deleted. The attempts to cater to audience tastes backfired as the new edits and scenes created continuity errors and major story problems.
In an interview with Ain't It Cool, Frank Oz's take on the film was "I f***ed up... I had too much money, and I was too responsible and concerned for Paramount. I was too concerned for the producers. And I didn't follow my instincts."
Director Frank Oz considered the idea of filming cameos with actresses Katharine Ross and Paula Prentiss, who appeared in the original film. He voted against the idea, citing that it would disrupt the credibility of the film.
Reports of problems on-set between Frank Oz and Nicole Kidman, Bette Midler, Christopher Walken, Glenn Close and Roger Bart were rampant in the press. Oz confirmed in an interview that there was "tension on the set" and that he had "had words" with Walken. He also blamed Midler for being under a lot of stress from other projects - she "made the mistake of bringing her stress on the set".
During post-production, in March 2004, a new scene was filmed: this scene showed Manhattan business women on their way to work, in congested Manhattan morning traffic. This was intended to be the "new" opening scene of the movie, directly preceding the Network Affiliate scene. This scene was later completely scratched from the film, before the official June 2004 release in theatres.
Several scenes and some sub-plots were deleted and/or added to the film based on audience test reactions: - The scene where Faith Hill's character breaks down at the square dance ran a few seconds longer. - There was originally a scene of Walter contemplating whether or not he should go through with turning Joanna into a Stepford Wife, and the other husbands try to convince him that she'll be happy that way. - Filmed but deleted was an extravagant extended version of the scene between Bobbie and Joanna when Joanna finds out that Bobbie has been turned into a Stepford Wife. After Bobbie tells Joanna all of her shortcomings, Joanna stabs Bobbie above the breast with a butcher knife. Bobbie goes haywire, and sets about performing a number of household tasks in the manner of the old Tex Avery cartoons, with Bobbie's finger turning into a vacuum cleaner, her tongue into a squeegee and her head exploding off of her shoulders while demonstrating what an orgasm is like for a Stepford Wife. The scene concludes with Bobbie opening her breasts to reveal a built-in cooler and offering Joanna a beer. It was the biggest FX sequence in the film, but was cut out despite great expense and months of work by computer artists. This was done because preview audiences felt it was "too much". It can be found as a deleted scene on the DVD. - An extended scene of Walter in the basement of the men's club deactivating the Stepford program, and displays indicate that the women's real brains have been transplanted into robot bodies. At the end of the sequence Faith Hill's character shoots her hand out of her arm on a long robotic tether and holds her husband up in the air. - The original ending of the movie was an extension of the scene where Glenn Close kisses Christopher Walken's head. When she kisses it, the electricity throws Close up in the air, where she levitates, as in the old Tex Avery cartoons, and her shoes explode off of her feet and fly up against a wall and all of her hair stands on end. She falls down next to Walken's head, which briefly comes alive and croaks, "Good night. Thank you for visiting Stepford," while Joanna and Walter look on and the camera pulls back for the fade-out.
Matthew's character, while fighting with his wife (played by Nicole), says he 'can't keep fighting with her...' and "game over." This was an obvious nod to his role in "Wargames" (1983) where he plays a boy fighting a computer to "end the game."