Director Shûsuke Kaneko cast Hideyo Amamoto as the prophet Isayama because of his guest appearance in the final episode (#28) of the TV series Urutora Q (1965), which Kaneko wanted to do a sequel to since the '80s.
The classic Toho monsters Anguirus and Varan were originally considered by writer/director Shûsuke Kaneko besides Baragon, but Toho asked Kaneko to replace the two with King Ghidorah and Mothra because Anguirus and Varan were not considered marketable (Ghidorah, Mothra and Baragon are among the most popular of the Toho monsters next to Godzilla). However, before this change, concept maquettes of Anguirus and Varan as they would've appeared in this film, were made by the film's monster designer, Fuyuki Shinada.
In addition to having the monsters Anguirus and Varan (instead of King Ghidorah and Mothra), the original story for the film featured rather outlandish military hardware, including batallions of Maser Tanks and a new version of the super-submarine Atragon (from _Atragon (1963)_).
Originally scheduled for a March 2002 release, upon the request of director Shûsuke Kaneko, Toho pushed it ahead for the usual release date for Godzilla films (December of 2001) because March already belongs to their Doraemon anime films (According to Toho, they take a seasonal formula for their films: Spring is for Doraemon, Summer is for Pokemon, and Winter is for Godzilla, so they didn't want any schedule conflict with their films).
During the scene where Godzilla first appears rising from Yaizu Harbor in Shizuoka, three people in a nearby office witness the incident (before Godzilla's thundering roar shatters glass on the office windows). Next to one of the three people, the camera focuses on a black and white poster of an old ship, the Lucky Dragon, which was the real life Japanese fishing boat that was contaminated by radioactivity in mid-1954. That incident became a direct inspiration for the original Godzilla (1954).
This was the first film since Mothra vs. Godzilla (1964) to portray Godzilla as truly evil. Director Shûsuke Kaneko preferred the original "evil" Godzilla for his film, and comes up with an unusual motivation (Godzilla, a monster brought to life by nuclear weapons, is a "specter of war").
Only Godzilla film of the six-film "Millennium" series (1999-2004) in which stuntman Tsutomu Kitagawa does not play Godzilla. Instead Godzilla is played by another stuntman, Mizuho Yoshida (best known as the title creature from the Zeiram movies), mostly for his height (Godzilla was to be the tallest monster in the movie).
In the opening scene, Admiral Tachibana (Ryûdô Uzaki) lectures his troops on the incident from Godzilla (1954), and notes that "a monster similar to Godzilla ravaged New York at the end of the last century." This was a reference (and jab) to Godzilla (1998), the oft-disparaged Hollywood remake. Audiences in Japan both laughed and cheered at this scene.
As a departure from the established Mothra mythos, the diminutive and singing Shobijin Twins (aka Cosmos Twins) seem to be absent. In fact, the twins Ai Maeda and Aki Maeda make a small cameo as two identically-dressed twins, seen during the scene where Mothra flies over Yokohama. Their roles are not related to Mothra in the movie, but that bit is a clear nod to the classic Shobijin.
The casting of Yukijirô Hotaru in a cameo as the suicidal man who discovers Ghidorah is a nod to his character of the beleaguered Inspector Osaka in all three of director Shûsuke Kaneko's Gamera films.
The pink-shirted young man (wearing a black baseball cap) standing behind the twin teenage girls in Yokohama when Mothra flies over the area. Yoshida is also the stuntman playing Godzilla.