Deleted Scene: An unfinished scene that was filmed shows that Destoroyah was to have the ability to fire an energy beam from his chest known as the "Wave-Motion Ray". He was to fire it 1-2 times on Godzilla with it. It was ultimately scrapped due to it's little usage in the film. This explains the mandible crevasse in his chest.
The original story was Godzilla fighting his predcessor in a form of a ghost (the 1954 Godzilla by the way), but the idea's been scrapped due to the idea of two of Godzilla's enemies being another Godzilla or Godzilla-like monster had already had its use. So now, they used the elements of the original film, and made out a monster born from the very weapon that killed the first Godzilla. Anguirus was originally to be a part of this scrapped idea as a guest character. The Ghost Godzilla idea was later revisited into Godzilla, Mothra, King Ghidorah: Giant Monsters All-Out Attack!.
Another idea that ultimately morphed into this movie was an idea known as "Godzilla vs. Barubaroi," a film in which Godzilla (who wasn't having a meltdown) and Junior were to fight a shape-shifting monster known as Barubaroi. The best way to describe this idea was what if Godzilla fought the Thing (and no, not that Thing...)
Junior's resurrection was originally a stinger, but Toho felt no one would see the scene by the time the film was over. So it was put as a final scene.
Originally, the plan for the series following this film was to take a break and let the American series run. Then, Toho would resume making new films in 2005. Of course, the 1998 remake was a disaster, so Toho brought Godzilla out of retirement six years early.