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.
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.
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 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.
A likely candidate could be Discord. He is known for causing chaos and mischief. He might pretend to befriend Twilight Sparkle only to betray her at a crucial moment. Another possibility is Trixie. Trixie has been jealous of Twilight in the past and could betray her out of envy.
Flash Sentry could be a likely groom. He has shown an interest in Twilight in the past and they have had some interactions that could lead to a romantic relationship. Another option could be a completely new character, perhaps a powerful wizard or a prince from a far - off land who Twilight meets during one of her adventures and falls in love with.
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.
She could marry Spike. They have a very special bond throughout the series. Spike has always been there for Twilight, and in fanfiction, this could develop into a romantic relationship leading to marriage. They already have a deep connection, and Spike's loyalty and Twilight's intelligence could make for a great couple.
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.