A corrupted version of a character they know. For example, a future Zoro who has turned evil due to some dark influence. He would be a formidable enemy as he already has great skills and knowledge of the Straw Hat Pirates' ways, and now he is working against them.
An ancient sea devil who was sealed away in the past but is awakened by their time - traveling. This devil could have the power to manipulate time itself and tries to stop Luffy and Nami from returning to their own time or achieving their goals.
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.
It could be a time - traveling version of Blackbeard. Maybe he also discovers time travel and uses it to his advantage to stop Luffy at every turn. He could go back in time and try to prevent Luffy from getting important allies or Devil Fruits.
It could be a time - traveling pirate who has his own evil plans for the past. He might be trying to change the past to gain ultimate power in the future. So he becomes an obstacle for Luffy who wants to either preserve the past or make positive changes.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
The Marines could be antagonists. They might see the baby as a threat or something that needs to be taken away from Luffy and Nami's crew. Maybe they think the baby has some connection to a dangerous pirate or revolutionary. The Marines would try to capture the baby and arrest Luffy and Nami for having it.
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.