Maybe it's a group of ex - ANBU members who have gone rogue. They know Hinata's importance to Naruto and Konoha. Their motives could be revenge against the village for some past wrongs. They think that by kidnapping Hinata, they can make Naruto and the village suffer.
It could be a group of rogue shinobi from a neighboring village who are jealous of Konoha's power and see Hinata as a valuable hostage. They might think that by kidnapping her, they can gain some leverage over Konoha in terms of resources or territory.
Perhaps a dark guild that has been observing Fairy Tail for a long time. They see Mirajane as a valuable asset and believe that her powers can help them in their evil plans. So they plot to kidnap her and force her to cooperate.
One possible kidnapper could be a rival engineer who is jealous of MacGyver's fame and ability to solve problems so effortlessly. This person might think that by kidnapping MacGyver, he can steal his ideas and take credit for his inventions. Also, it could be a group of eco - terrorists who believe MacGyver's work has been harmful to the environment in some way and want to force him to make amends by using his skills for their cause. A third option is a deranged fan who has an unhealthy obsession with MacGyver and wants to keep him all to himself, thinking that kidnapping is the only way to have MacGyver's undivided attention.
The Akatsuki is also a possibility. They are after jinchuriki, and if they knew about Naruto's existence as a baby, they might try to kidnap him early. They could think that by having him from the start, they can better control the Nine - Tailed Fox within him.
A powerful and vengeful warlord from a forgotten realm could be a kidnapper. He might see Wonder Woman as a threat to his plans of conquest and decides to take her out of the picture by kidnapping her.
One possible motive could be to use Hermione as a bargaining chip against Harry Potter. Since Hermione is his close friend, the kidnappers might think they can force Harry to do something, like give up a powerful magical item or valuable information.
One possible motive could be power. If Naruto has some unique abilities or is a key to something powerful in the fanfic world, the kidnappers might want to control him to gain that power for themselves.
Another possibility is some disgruntled former employees. Maybe they feel they were wronged by Stark and want to get revenge. They know his routines and weaknesses well enough to plan a successful kidnapping.
Another possibility is a werewolf who has lost control or has a different agenda. In the Twilight universe, the werewolves and vampires have a tenuous relationship, and a werewolf kidnapping Bella could add a whole new layer of conflict. It could be a werewolf who doesn't trust Bella's relationship with the vampires and thinks she's a threat to their pack in some way.
A new, evil sorcerer who has just arrived in Narnia could be the kidnapper. He might have heard tales of Lucy's importance and figure that by taking her hostage, he can control the forces of good in Narnia. Or perhaps a tribe of wild centaurs who have been corrupted by some dark magic might kidnap Lucy. They could be under the influence of a spell that makes them believe Lucy is the cause of all their problems and that getting rid of her will solve everything.
Perhaps an old enemy of Igneel, Natsu's dragon father. They might see Natsu as a way to get revenge on Igneel. They think that by torturing Natsu, they can somehow hurt Igneel even though he's not around. Or it could be a group that is after the secrets of dragon slayer magic and believe Natsu has the key to unlocking those secrets.