Well, you could have a fanfic where the Pokemon regions are somehow connected to the Hidden Villages in the Naruto universe. For instance, the Leaf Village could be near the Kanto region. And then there could be a plot where a new type of threat emerges that requires the combined efforts of both Pokemon trainers and ninjas. Also, characters from both series could swap abilities. Imagine Sasuke using Pikachu's Thunderbolt or Ash using Sharingan to predict his opponents' moves in Pokemon battles.
A really fun Naruto Pokemon fanfic concept would be a story centered around a Pokemon tournament in the Hidden Leaf Village. Naruto and his friends would enter the tournament with their Pokemon partners. They'd have to train their Pokemon in the ways of the ninja, teaching them things like stealth and quick - thinking. And at the same time, the Pokemon would teach the Naruto characters some of their unique skills, like how to communicate with nature better through the Pokemon's connection to it.
One idea could be a story where the trainers of Pokémon and the Tamers of Digimon have to team up to save both their worlds from a common threat. Maybe a powerful virus that affects both Pokémon and Digimon data.
One idea could be a story where a human trainer has a special bond with a Pikachu that allows them to communicate telepathically. Another could be a human getting lost in the Pokemon world and having to team up with various Pokemon to find their way back home. Or perhaps a story about a human who discovers they have the power to transform into a Pokemon.
Another interesting concept could be the Pokemon in the Naruto world having chakra. So, they can use ninjutsu-like moves. Imagine a Charizard using a fire - based ninjutsu attack. Also, the Pokemon could form bonds with the ninja clans in the Naruto universe, like the Uchiha clan having a special connection with dark - type Pokemon.
One idea could be that Naruto is transported to the Pokemon world. He might use his ninja skills to catch Pokemon in unique ways, like using his shadow clone jutsu to surround and corner a wild Pokemon. Another could be that Pokemon are introduced to the Naruto universe, and ninjas start to form bonds with them to enhance their combat abilities.
A third idea is that the reader is a Pokemon trainer who has lost their memory. They wake up in a Pokemon center with no recollection of who they are or what their Pokemon are. With the help of the Pokemon center nurse and their own Pokemon, like a Pidgey, they start to piece together their past. As they travel around to different places looking for clues, they encounter various challenges and make new friends, both human and Pokemon.
One idea could be that Naruto somehow gets transported to the Pokemon world and meets May. They could go on a journey together to find a way for Naruto to get back home while also helping May achieve her Pokemon goals. For example, Naruto's skills in combat and strategy could be useful in Pokemon battles.
Another interesting concept could be a story about Naruto visiting Starfire's world. He could be amazed by the different technology and culture there, while Starfire is intrigued by Naruto's ninja skills and his chakra.
Another idea is a 'what - if' scenario. For example, what if Boruto was raised in a world where Naruto had failed to become Hokage? This could lead to a very different Boruto, perhaps more cynical or desperate to change the world on his own. The fanfic could explore how he would grow up and try to fix the situation his father couldn't.
A Naruto x One Piece crossover would also be cool. Naruto could end up on the Grand Line and team up with the Straw Hat Pirates. His ability to create shadow clones could be useful in battles against other pirates, and he might learn some new skills from Luffy and the crew.