Itachi might be a strong contender. His calm and calculating nature would serve him well in the Pokemon world. He could choose a Psychic - type Pokemon like Alakazam. Itachi's Sharingan would give him an edge in battles, allowing him to predict his opponents' moves. And with Alakazam's high intelligence, they could come up with complex battle plans that would be hard for others to counter.
Definitely Naruto himself. He has an unwavering will and determination. If he had a Pokemon like Charizard, their combined strength would be incredible. Naruto's ability to make friends and form strong bonds could also make his relationship with his Pokemon very deep. He could use his ninjutsu in combination with his Pokemon's attacks, for example, using his Rasengan while his Pokemon distracts the enemy.
In a fanfiction battle, it also depends on how the characters adapt to each other's worlds. For example, if Naruto learned how to play Yugioh and could use his ninja skills to quickly draw and play cards, he could be very powerful. Similarly, if a Yugioh character like Joey learned some ninja techniques, he could be a formidable opponent in the Naruto universe.
Sasuke. He already has powerful Sharingan abilities. With the Omnitrix, he could add alien powers to his already formidable skills. He could use the speed of an alien form to enhance his own movement speed during battles and combine it with his Chidori attacks for even more devastating strikes.
It could be Yubel from Yugioh GX. Yubel has incredible power and is very difficult to defeat. With her ability to possess and manipulate, she could be a tough opponent for Naruto characters.
It's likely that Naruto himself would be one of the most powerful. His ability to use chakra and perform powerful jutsus like the Rasengan would give him a huge edge in the ring. He could quickly build up momentum and deliver devastating blows to his opponents.
Arceus from Pokemon and Omnimon from Digimon are both extremely powerful. Arceus is like a god in the Pokemon world, creating everything. Omnimon is a powerful Digimon formed by the fusion of WarGreymon and MetalGarurumon. If they were in a crossover, it's really hard to say who would be more powerful. It might depend on the situation and how their powers interact.
Another possibility could be Chara. In undertale, Chara has a complex and somewhat malevolent nature. If they were in a pokemon crossover, they might find a way to manipulate pokemon or use their determination - related powers in a way that makes them extremely powerful. They could potentially form alliances with dark - type pokemon or use their knowledge of the undertale world to outwit opponents in the pokemon world.
It could be Hiccup if he manages to form a strong bond with a really powerful Pokemon like Mewtwo. Mewtwo has incredible psychic powers, and if combined with Hiccup's strategic mind and his ability to understand and work with Toothless, they could be an unbeatable team.
Perhaps Naruto combined with Toph. Naruto's agility and combat skills along with Toph's earthbending mastery would be quite a combination. Toph could sense enemies from afar using her earthbending senses and Naruto could quickly engage them in combat. Also, Naruto could use his clones to help Toph with larger - scale earthbending projects, like building massive structures for defense or offense in a battle.
Another candidate could be Dialga from Pokemon. Dialga has the power to control time. In a crossover, if it could use its time - control abilities effectively against the Dragonball Z characters, it could be very powerful. For example, it could freeze time and then attack its opponents without them being able to react. But again, Goku has shown the ability to break through all kinds of limitations, so he might still find a way to defeat Dialga in the end.
Probably Natsu. Natsu has his own dragon - slayer magic which is already very strong. If he were to bond with a legendary Pokemon like Rayquaza, he could become almost unbeatable. Rayquaza's flying and powerful attack abilities, along with Natsu's fire - based attacks, would create a terrifying combination in battles.