Franchise Killer: Toho decided to make Final Wars as a Grand Finale to the Millennium era while they put the franchise on temporary hiatus. Of course, even if they hadn't planned to shelf the King of the Monsters for the time being, they probably would've done so anyway after Final Wars ended up being the lowest-grossing of all the Millennium films.
A very mild case, Kiryu, Gorosaurus, and KING GHIDORAH (who Monster X would've transformed into instead of Kaiser Ghidorah) were all slated to appear in the film as well. Unfortunately, none of them made the cut, and Kiryu and Gorosaurus were replaced by the Gotengo and Zilla.
Additionally, the film was initially intended to be a follow-up to the Heisei series with the film's Godzilla being the adult Junior. Since one idea was for the finale to have Destoroyah instead of Kaiser Ghidorah, this could have made for a great confrontation, as Junior would want revenge on Destoroyah for killing him.
Godzilla was to actually kill Rodan, Anguiurus, and King Caesar, but this was ultimately changed to him sparing them as a nod to his friendly relations with them in the past. And also because they'd already lost the suits without filming it.