It could be a super intelligent pirate who has been secretly controlling events in the One Piece world. This antagonist might be several steps ahead of everyone, creating elaborate plans to take over the Grand Line. Luffy, with his newfound intelligence, has to match wits with this foe.
Perhaps an old enemy of the Straw Hats who has become much smarter. For example, Buggy the Clown could return but with a more devious and intelligent plan to take revenge on Luffy. He could have studied Luffy's fighting style and weaknesses and uses this knowledge to try and defeat him. But Luffy, being smart, can see through Buggy's tricks.
The World Government could be the main antagonist in a more complex way. They could be secretly manipulating events to pit Dragon and Luffy against each other. For example, they could spread false rumors about Luffy being a tool of the revolutionaries, which would make other pirate crews and kingdoms target him, and at the same time make Dragon look bad for having a son who is causing so much chaos. This would force Dragon and Luffy to either fight each other or find a way to clear their names together.
It could be a new character created specifically for the fanfiction. Maybe a powerful pirate who has a vendetta against the Straw Hat crew because of the oc's presence. Since the oc is reborn into this world, they might bring some sort of change that angers this new antagonist.
A powerful new pirate group could be the main antagonist. They might be after the same treasure or territory as Luffy and Shanks. They could have some unique and dangerous abilities, like the ability to control sea monsters. Their leader could be a former crewmate of a well - known and feared pirate, who has his own vendetta against both Luffy and Shanks for some past reasons.
It could be a lemon - loving pirate who has a grudge against Luffy for some reason. Maybe Luffy accidentally destroyed his precious lemon grove on an island. So this pirate, with his crew of lemon - themed fighters, constantly tries to sabotage Luffy's adventures and steal his treasures.
A time - traveling pirate who has his own agenda and wants to change the course of pirate history for his own gain could be the antagonist. This pirate might be jealous of Luffy's future achievements and try to stop him from ever becoming the Pirate King by changing things in the past.
A powerful dragon - themed pirate could be the main antagonist. This pirate has a crew of dragon - like creatures and they are causing chaos across the seas. They have a grudge against Luffy for some reason, perhaps because Luffy has unknowingly entered their territory or stolen something valuable from them.
The World Government could be the main antagonist. They see both Luffy as a growing threat to their rule as a pirate and Dragon as a revolutionary. When Luffy and Dragon meet, the World Government might send their strongest agents like the Admirals to stop them from joining forces. The World Government's strict control over the world and their desire to maintain the status quo would put them in direct opposition to Luffy and Dragon.
A powerful and corrupt World Noble could be the main antagonist. They might be trying to stop both Luffy and Dragon's efforts for freedom. The World Noble could have a large military force under their control and be causing chaos and oppression in various parts of the world. This would force Luffy and Dragon to join forces to take them down.
The main antagonist could be a mean-spirited mole. This mole is constantly digging tunnels under the garden and causing chaos. He doesn't like Gnomeo and Juliet's love because he believes it's disrupting the natural order of the garden. He tries to separate them by causing misunderstandings between their families.
An organization that believes in using Pokemon for dark magic could be the main bad guy. They see Iris and her Pokemon as a threat to their plans, so they constantly try to stop her. They might have their own powerful, corrupted Pokemon that they use to battle Iris. They could also be stealing Pokemon from other trainers to use in their dark experiments.