You could focus on the backstory of the pilots who control the mechs in Godzilla Kaiju Wars. For example, a young pilot who has to overcome personal traumas from past Kaiju attacks to be able to face the new threats. Or perhaps write about a team of scientists who are trying to develop a new weapon to defeat the Kaiju once and for all. They might face ethical dilemmas as they test their new creations on smaller, less dangerous Kaiju.
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.
One idea could be a kaiju fanfiction where the kaiju form an alliance with humans to fight against an even greater threat from outer space. It would be a unique twist on the usual kaiju - human conflict.
One idea could be a story where Godzilla teams up with other kaiju from different universes to fight a new, super - powerful alien threat. This would bring in a whole new level of epic battles and interactions between the various monsters.
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.
One interesting idea could be the RWBY characters having to team up in new ways to combat the kaiju. For example, Ruby's speed might be used to quickly dodge a kaiju's attacks and find its weak spots. Another idea is the fusion of Dust technology with kaiju - like elements. Maybe they create new weapons that can both harm the kaiju and also harness some of their power. Also, the idea of kaiju having Aura or semblances of their own could be really cool, changing the dynamics of how the RWBY characters interact with them.
One idea could be a human who gains kaiju - like powers through a scientific experiment gone wrong. They then have to deal with the consequences of their newfound strength and the fear of society. Another could be a world where humans and kaiju co - exist, and a human befriends a kaiju and they go on adventures together. A third idea is a group of humans who have to fight off an invasion of kaiju using their wits and some stolen kaiju technology.
One idea could be a fanfic where the main character has a unique power to communicate with the kaiju. This would add a new dimension to the story as they could try to negotiate with the kaiju instead of just fighting them.
One idea could be a story where Little Godzilla teams up with other baby kaiju to protect their island home from human pollution. They use their small but growing powers to clean up the mess and teach humans a lesson about respecting nature.
One idea could be a Godzilla crossover with King Kong. They could start off as enemies but then have to team up to fight a common, greater threat like an alien invasion. This would bring in the classic monster -vs- monster dynamic at first and then shift to an alliance against a new foe.
One idea could be Godzilla emerging in the world of RWBY and the Huntsmen and Huntresses having to figure out how to deal with it. Maybe they initially mistake it for a new type of Grimm.
How about a Godzilla crossover with the Avengers? Maybe in a world where the Avengers exist alongside the Kaiju. Godzilla could be seen as both a threat and an ally. Iron Man could try to study Godzilla's power source while Thor might see him as a kind of primordial force. Captain America would be the one trying to keep everyone in line and figure out how to co - exist with this giant monster.