It could be the well - known Team Rocket. They are always up to no good and kidnapping Pokemon for their own gain is right up their alley.
Perhaps a new, shadowy organization that has emerged in the Pokemon world. They might have some ulterior motives like trying to gain power over a certain region by using the kidnapped Pokemon as leverage.
Perhaps a powerful and corrupted Pokemon could be behind the kidnapping. This Pokemon might be under the control of an evil force or it could have its own motives. It could sense Lillie's special connection to Pokemon and want to use her for its own gain, like increasing its power or finding a way to rule over other Pokemon.
A group of poachers could be the kidnappers. They might think that Serena has information about the location of rare Pokemon in the areas she has traveled. They want to use her to find these Pokemon so they can capture and sell them on the black market.
It could be Vilgax. He has always been after the Omnitrix and kidnapping Ben 10 would be a way for him to get it.
Well, it could be a secret organization that has been operating in the shadows. They might have some ulterior motive related to Naruto's power or his connection to the Nine - Tails. Maybe they believe that by kidnapping Naruto, they can control the Nine - Tails and use it for their own purposes. Another option is a jealous ninja from within Konoha. This ninja might feel overshadowed by Naruto's achievements and popularity and decides to kidnap him to get him out of the picture. Also, a powerful and ancient being awakened from a long slumber could be the kidnapper. They see Naruto as a source of energy or a key to something they desire.
It could be a jealous rival from his past. Maybe someone he outperformed in a competition or a former acquaintance who has a grudge against him.
It could be Death Eaters who are still lurking in the shadows. They might see Hermione as a threat because of her association with Harry Potter and her strong stance against the Dark Arts. They could kidnap her to try and get information about Harry or to use her as bait.
Another option is a random criminal who just sees May as an easy target. He might not even be related to the Pokemon world initially but realizes that he can ransom her to her wealthy Pokemon - loving family or friends. However, he soon finds out that dealing with a Pokemon trainer's friends is not as easy as he thought.
It could be a rogue ninja who wants to use Boruto to get to Naruto. Maybe someone who has a grudge against the Hokage.
It could be Luke Castellan. He has a history of being against Percy and the Olympians. He might kidnap Percy to gain an advantage in his own quest for power. He could use Percy as a bargaining chip with the Titans or other powerful forces.
It could be Orochimaru. He's always been interested in Sasuke and might see kidnapping Sakura as a way to manipulate Sasuke. He could use Sakura as a guinea pig for his experiments or as a bargaining chip to get Sasuke to come to him.