A rogue ninja from another village who is jealous of Ino's talents and the reputation of her village could be the villain. This ninja might think that by kidnapping Ino, they can bring down the morale of her village and prove their own superiority.
Perhaps a group of bandits who have heard of Ino's value as a ninja. They might not fully understand her abilities but know that she is important to her village. So, they kidnap her with the hope of getting a large ransom or some other form of valuable compensation from her village.
The villain could be a jealous ice - mage who wants Elsa's powers all to himself. He sees Elsa as a threat to his own dominance in the world of ice magic.
It could be Orochimaru. He might be interested in Ino's unique abilities, like her mind - control jutsu, for his own evil experiments. So he kidnaps her, and Naruto has to fight against Orochimaru's snake - like techniques to save Ino.
A jealous vampire could be the villain. Maybe a vampire who has always desired Bella for herself. She sees Edward as an obstacle, so she kidnaps them both to get Bella away from Edward and have her all to herself.
In a more fantastical setting, it could be a magical being who has some sort of vendetta against Peter or Michelle. Maybe they accidentally disrupted some magical ritual or offended the being in some way, and now the being wants to use their kidnapping as a form of punishment or to get something from them.
A mad scientist - type character could be the villain. He might be obsessed with creating the perfect virtual being and sees Hatsune Miku as the key. So, he kidnaps her to run all kinds of experiments on her code. He wants to extract her unique singing ability and transfer it to his own creations.
It could be a new villain who is trying to make a name for themselves by targeting a popular hero like Present Mic. They might see him as an easy target to get attention.
It could be a vengeful criminal that Neal put away in the past. This person has been planning their revenge for a long time and finally sees the opportunity to kidnap Neal.
It could be a group of outcast Lost Boys who have turned bad. They might be jealous of Wendy's special place in Peter's heart and in the group. So they kidnap her in an attempt to show Peter that they are in control now and can disrupt the harmony of the group.
The Vulture could be a likely villain. He might see kidnapping a Spider - Man fan as a way to draw Spider - Man out into the open and then attack him when he's vulnerable trying to rescue the fan. The Vulture could be after some valuable tech that he believes Spider - Man has hidden and thinks the fan might know its location.
The Joker is a likely suspect. He loves to target Batman's loved ones to mess with him. He might use the kidnapping as a way to draw Batman into a twisted game, setting up elaborate traps along the way.