One idea could be to write a story from the perspective of a civilian caught in the middle of the Kaiju battles. Show their fear, their attempts to survive, and how they interact with the military trying to stop the Kaiju. Another could be a story about a Kaiju that has unique abilities not seen in the original lore, and how it changes the dynamic of the wars. Maybe it could be a Kaiju that can communicate with humans and tries to form an alliance against the more destructive Kaiju.
Some of the lesser - known Kaiju can also be interesting to include in fanfiction. For example, Rodan. He has his own unique abilities and personality. A fanfiction could explore his backstory more deeply, or create a new relationship between him and the other more well - known Kaiju. Anguirus is another one. He could be portrayed as a loyal ally to Godzilla, or have his own motives for being involved in the Kaiju Wars.
In fanfiction, Godzilla could be a protector of the Earth in a different way than the Avengers. The Avengers protect the people from threats, while Godzilla protects the balance of nature. So, when an alien race starts to mine the Earth's core in a way that disrupts the planet's stability, Godzilla appears. The Avengers at first misunderstand Godzilla's intentions. But as they see the real threat, they join forces with Godzilla. Godzilla's size and strength would be a huge asset against the technologically advanced alien invaders. The Avengers could also learn from Godzilla about the Earth's natural defenses.
One possible Pokemon Godzilla fanfic could be about a group of trainers who accidentally stumble upon a Godzilla - like Pokemon in a hidden, uncharted region. This Pokemon could have the immense power of Godzilla, causing chaos and also attracting the interest of both good and bad organizations within the Pokemon world. The trainers then have to decide whether to try and capture it or find a way to calm it down.
Well, it's possible that such a fanfic exists. However, without actually scouring every single MLP - related fanfic site, it's hard to say for certain. Maybe it was created by a very creative individual who wanted to combine the rather unexpected elements of Godzilla and MLP. But again, I can't confirm its existence without further research.
Well, it could mean a whole new generation of Mutos. Maybe they would be stronger or have different abilities. It might also change the power balance in the Godzilla universe. For example, if the baby Mutos are aggressive, they could start attacking other creatures more often, causing chaos.
Godzilla also has a certain level of durability. In the MHA world, quirks that can penetrate or bypass such extreme durability would be highly valued. On the other hand, Godzilla's presence could inspire the development of new support items or quirks that are specifically designed to deal with large and powerful threats like him.
Kaiju novels often portray kaiju as gigantic and powerful beings. They are usually depicted as forces of nature that are difficult to control or defeat. For example, in 'Godzilla' novels, Godzilla is shown as a nearly indestructible creature with its atomic breath and massive size.
One popular 'kaiju x kaiju fanfic' story could be about Godzilla and Mothra forming an alliance in a unique way. Maybe they team up against a new, more powerful enemy that threatens their world.