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.
One popular character might be a kaiju girl with the ability to fly. Her aerial battles against other kaiju or threats are often a highlight in many fanfics. She is usually depicted as strong and independent.
Godzilla might see the pregnant Muto as a threat. After all, Mutos are his enemies. So he could start hunting it down to prevent more Mutos from being born.
Naruto would probably be both amazed and a bit scared at first. But being Naruto, he would quickly jump into action. He might try to use his rasengan against Godzilla, thinking it could do some damage. However, he would soon realize that Godzilla is much more powerful than he initially thought and would have to come up with a different strategy, like using his speed to avoid Godzilla's attacks and find its weak points.
A kaiju girls fanfic could also explore their origin stories. Maybe they were created by some scientific experiment gone wrong. The fanfic could delve into how they feel about their existence, whether they resent being different or embrace their kaiju side, and how they interact with the scientists who were involved in their creation.
Shinji would probably be terrified at first. He's already hesitant and scared in his normal battles, and Godzilla is much larger and more intimidating than the Angels he usually faces. Asuka would likely be more aggressive, thinking she can take on Godzilla with her Eva. Rei, on the other hand, would be very calm and observant, trying to understand Godzilla's nature. Misato would be in a panic initially, but then quickly start strategizing on how to deal with this new threat. Gendo would see Godzilla as either a new opportunity or a major obstacle depending on his long - term plans.
Some of them might be amused. For instance, Hulk could find it funny if Godzilla was shown as being weak in the fanfiction. He might laugh and say 'That big lizard not so tough!'.
Some of them would be amused. Hawkeye might chuckle at the outlandish scenarios in the fanfic. Black Widow would be more reserved but still interested. She'd be quietly observing and thinking about the implications of the story. Captain America would try to find the moral of the story, if there is one, as he always does.
Ruby would probably be both scared and fascinated. She's always been curious about new things, and Godzilla is definitely something new. But she would also be worried about the destruction it could cause. Weiss might be more cautious and initially see Godzilla as a threat to the order in Remnant. Blake would likely be on guard, observing Godzilla's behavior to see if it's truly hostile or not.