Contest Winner Cameo: The entire script, though it was changed so much only the following aspects were kept: the death of Dr. Shiragami's daughter, Biollante's creation, a psychic girl, and the general ending.
Deleted Scene: A scene in the movie where Godzilla first approaches Biollante, she would retreat and release spores that grew flowers. Godzilla is surprisingly calmer looking than he actually is, even seeming to cry.
Biollante is also shown to indiscriminately kill a JSDF investigation squad in another.
Troubled Production: A less serious version, but still there. After The Return of Godzilla, Tomoyuki Tanaka wanted a direct sequel to be made. However after hearing King Kong Lives bombing, he was cautious on how the series would be handled. Kazuki Omori, who became director of the film, had a Teeth-Clenched Teamwork relationship with him (he blamed Tanaka for the quality of the series in the 70's like Ishiro Honda did, but Honda is more respectful about it. Akira Ifukube on the other hand...). They both settled on making a contest with five entries, one mentioned below, and Omori then decided to modify the screenplay (which took 3 years) until the film became what it is.
The film was originally written by Shinichiro Kobayashi (a dentist) and featured a far different story than what the film is today. The film was to focus heavily on Dr. Shiragami as he creates both Biollante and a rat/fish hybrid monster named "Deutalios" out of insanity due to his daughter Erica's death. Godzilla would've fought, killed, and eaten Deutalios and would've fought Biollante until retreating due to injuries. However it was felt that Godzilla was given very little focus in the story, and so re-writes were made: replacing Deutalios with the Super-X2 and a rose form of Biollante, and Godzilla being injected with Anti-Nuclear Bacteria to slowly kill him.
In the script and or an earlier draft, Miki was supposed to psychokinetically levitate Godzilla, but Tomoyuki Tanaka apparently wasn't fond of the idea.
In another ending, a losing Biollante would have tried to kill Godzilla by turning into a wave of pure energy.
One idea for Biollante's final design in the film was a flower with human face in the middle that talked.