Author Tract: Due to the director's long time pacifist beliefs, the movie is very critical of modern Japan's outlook on the Pacific War, with it being outright stated that Godzilla is being fueled by the spirits of those killed by the Imperial Army.
Awesome Music: It's quite different from other soundtracks in the franchise, but Kow Otani (also known for Shadow of the Colossus and the Heisei Gamera Trilogy) delivers an incredible score that's right at home with the atmosphere of the film.
Fridge Horror: The man attempting to hang himself in a Mount Fuji forest is most certainly the Aokigahara Forest, a popular suicide destination in Japan, or at least a direct reference to it. It's stated that the Guardian Monsters are empowered by souls, the same as Godzilla...and considering what forest it is, that man isn't the first to try and kill himself there, and King Ghidorah was sleeping in that forest. In other words, Ghidorah was absorbing the souls of the people who committed suicide there.
Godzilla is noticably...heavier in this film. Corpses swell after a certain amount of time, suggesting further that whatever the thing attacking Tokyo is, it's not a living Godzilla anymore.
The "Red Godzilla" lines in the movie later became a reality in one certain film...
At various points during the film's preproduction, Godzilla would've fought a CG version of Kamacuras and the Atragon warship in a heavily altered version of Japan, but Kaneko ultimately found the alternate history aspects distracted from the story he wanted to tell. All three elements would later be used in Godzilla: Final Wars.
Misaimed Fandom: Godzilla was meant to be an entity of pure evil in this incarnation. Didn't stop fans from rooting for him anyway.
This was because he was possessed by vengeful spirits, so we are not exactly sure if his conciseness was the same as the Anti-Hero in the first one.
Nightmare Retardant: This Godzilla suit has been widely criticized for being kinda fat. It's near impossible to keep a straight face when he runs while joggling his gut around. Further, some have realized he looks like◊ KingKoopa.
He was originally going to have Varan fill this role but Executive Meddling got in the way. Ghidorah's designer actually decided to put some of Varan's features into Ghidorah's heads.
Anguirus was going to have Mothra's role.
Rescued from the Scrappy Heap: In a very weird way given it's caused by a Take That, Scrappy!: a lot of fans find the confirmation that Zilla is a separate kaiju in this film makes him much more enjoyable a character by separating him and Godzilla from one another.
Some Anvils Need to Be Dropped: A nation can't just wipe away its past, it will come back to haunt them in some form or another. Takes on a lot more meaning when you realize how little Japan tries to acknowledge the events of WW2 in anything other than passing.
Several of Japan's atrocities are on par with the Holocaust, but are not common knowledge anywhere but the places where they were committed (China, the Philippines, Korea). As is stated in the film, it's not just Japanese servicemen who are out for revenge; it's everyone Japanese reckless drive for Empire destroyed.