One idea could be that the Pokemon have Quirks. For example, Pikachu could have an electric - based Quirk that is even more powerful than its normal electric attacks. The heroes in training from My Hero Academia could team up with these special Pokemon to fight against villains who are also using Pokemon with dangerous Quirks. It would be a really cool mix of the two universes.
One great 'My Hero Academia' crossover fanfiction is the one where they cross over with 'One Piece'. It combines the unique powers of the 'My Hero Academia' world with the adventurous and diverse world of 'One Piece'. The characters interact in really interesting ways, like Midoriya being amazed by Luffy's Devil Fruit powers and Luffy being intrigued by the concept of Quirks.
One idea could be that Kakashi is somehow transported to the My Hero Academia world. He could become a teacher at UA, using his ninja skills and wisdom to train the students in new and unique ways. His Sharingan would be a very interesting power in the MHA universe.
Deku would also be a great choice. Since he's always looking to grow and improve, having a Pokemon by his side could be a new way for him to develop his skills. He could bond with a Pikachu - like Pokemon that has an electric Quirk. The two of them could train together and face challenges side by side, and Deku could learn new things from the Pokemon's instincts.
One idea could be that Godzilla arrives in the My Hero Academia world during a major villain attack. The heroes initially see Godzilla as a threat but soon realize that he is targeting the same villains who are causing environmental destruction. His massive size and power could be a game - changer in the battle.
A great crossover idea is with the Dragon Ball series. The powerful Saiyans could interact with the My Hero Academia characters. Goku could train the students at UA to reach new levels of power. Also, a crossover with the Attack on Titan world would be intense. The heroes would have to deal with Titans in a whole new way and use their quirks in that battle - filled environment.
In some fanfictions, the Pokemon world and the My Hero Academia world might merge. This could lead to situations where the heroes have to deal with Pokemon villains. Like a villain using a powerful and evil - natured Pokemon to cause chaos in the city, and the heroes would have to use their Quirks and their newfound knowledge of Pokemon to stop them.
In this fanfiction, a cool concept might be the Pokemon evolving in response to the growth of the characters' Quirks. So, as a character becomes more powerful in their use of their Quirk, their Pokemon also evolves to a stronger form. Also, the idea of Pokeballs being modified to work with the technology in the My Hero Academia world, like having security features that only the owner's Quirk can unlock, is quite fascinating.
Here's a simple start for a 'prototype My Hero Academia crossover fanfic': In a world where the quirks of My Hero Academia exist alongside the powers from 'prototype'. Alex Mercer finds himself in the middle of Musutafu city. He's confused by the sight of people with all these strange abilities. Izuku Midoriya spots this strange man and approaches him. Mercer, being the shape - shifter he is, tries to blend in but his lack of knowledge about quirks starts causing some misunderstandings. As they interact, Mercer realizes that these 'quirks' could be a new form of power to study, while Midoriya is both fascinated and a bit scared of Mercer's abilities.
One idea could be a crossover with the Naruto universe. The characters from My Hero Academia could interact with Naruto characters. For example, Deku might learn some new fighting techniques from Naruto. Another idea is a crossover with the Harry Potter world. The students at U.A. could visit Hogwarts and experience magic, while the Hogwarts students could learn about quirks.