It could be a jealous rival of Esme. Maybe someone who is envious of her popularity or success.
Perhaps a group of outlaws who are looking for money. They might think that Esme's family is wealthy and they can get a large ransom for her. Another possibility is that it's a mad scientist who wants to use Esme for some kind of experiment. He believes that Esme has unique genetic traits that are valuable for his research.
The kidnapper could be an old enemy of Esme's family. They have a long - standing feud and see kidnapping Esme as a way to get revenge on her family. Or it could be a cult that believes Esme has some sort of spiritual significance and they want to use her for their rituals. There's also a chance that it's a deranged fan who has become obsessed with Esme and wants to keep her all to himself.
Perhaps it's an organization that wants to use Kakashi for their own evil plans. They might think that Kakashi's skills and knowledge would be useful for them. For example, they could be trying to create some sort of super - weapon and they need Kakashi's expertise in ninjutsu.
It could be Hades. He's always been an antagonist in the series and might kidnap Pit to mess with the gods. He could be thinking that by taking Pit, he can gain an advantage in his ongoing feud with them.
It could be a rogue Saiyan who wants to take over the Saiyan throne and thinks kidnapping Goku is the first step.
It could be a new villain that we haven't seen in the main Mario games. Maybe a powerful sorcerer who needs Mario for some dark magic ritual. This sorcerer might have been lurking in the shadows of the Mushroom Kingdom, waiting for the right moment to strike and kidnap Mario.
Maybe it's a new villain created specifically for the fanfiction. This new character could be jealous of Sora's popularity and power, and decides to kidnap him to prove their own worth. They might think that by capturing Sora, they can gain the respect of other villains or even take over the worlds that Sora has been protecting.
Maybe an enemy from another village. If there are political tensions between villages, kidnapping Sarada could be a way to gain an advantage. They might think that by having her, they can force her village to make concessions in treaties or resources.
It could be the Joker. He's always up to no good and kidnapping Robin would be a great way to mess with Batman. The Joker might want to use Robin to force Batman into a series of cruel and twisted games.
A new villainous trainer group. They might see Ash as a threat to their plans of dominating the Pokémon world, so they kidnap him to stop him from competing in important battles or tournaments.
Maybe it's a group of rogue Death Eaters who are still loyal to Voldemort's ideals. They believe that by kidnapping Ginny, they can disrupt the peace in the wizarding world and send a message to those who defeated Voldemort.
One possibility is Dr. Eggman. He has always been after Sonic and wants to stop him. Kidnapping Sonic would be a way for him to achieve his evil goals.