Maybe some mad scientist who wants to experiment on Beast Boy's shape - shifting DNA. He could be looking for a way to transfer the ability to himself or create some sort of mutant army. Another option is that it's a group of aliens who mistake Beast Boy for a dangerous creature and capture him to study. They might not understand that he's a sentient being with friends who will come looking for him.
It could be a powerful sorcerer. Beast Boy's shape - shifting abilities might be of great interest to a sorcerer who wants to use his power to enhance their own magic. The sorcerer might think that by capturing Beast Boy and performing certain rituals, they can extract and harness his unique power source.
Another possibility is a group of corrupted Plumbers. They turn against Ben and capture him, perhaps because they want to use the Omnitrix for their own evil purposes. They would have knowledge of Ben's abilities and how to contain him, which would make for an interesting conflict.
It could be Captain Hook. He has always been Peter Pan's nemesis and has a strong motive to capture him. Maybe he wants to finally get revenge for all the times Peter has outsmarted him.
It could be Discord. He loves causing chaos and might capture Twilight Sparkle just for the fun of it or to disrupt the harmony in Equestria.
Well, he could be rescued by his friends. Maybe Raven uses her magic to track him down and then the team like Cyborg and Starfire fight off the captors.
It could be Team Rocket. They've always been after Ash and his Pikachu. They might finally succeed in capturing him and then Pikachu has to come up with a plan to rescue Ash.
There's a possibility that it's a villainous trainer. This trainer might capture Gengar with the intention of using it for evil purposes, like using Gengar's powers to steal other Pokémon or cause chaos in Pokémon battles.
Maybe it's an old foe who has managed to regain power and wants to make Sora pay for past defeats. For example, a powerful dark sorcerer who was once defeated by Sora but has now found a way to capture him through some devious plot.
It could be the Blackbeard Pirates. Since they have a history with the Whitebeard Pirates, they might capture Marco to get information or as a form of revenge.
It could be Slade. Slade might manipulate situations to make Beast Boy look bad in front of his friends. He could spread false rumors or set up situations where Beast Boy fails, which would make Beast Boy angry at being wrongly accused and at the fact that his friends might start to doubt him.
Slade could be a great main villain. His combat skills and strategic mind would pose a huge challenge for Beast Boy. Beast Boy would have to constantly outwit and outmaneuver Slade, which would really bring out his badass side as he tries to protect his friends and the city from Slade's evil plans.