Perhaps an ancient evil force that was sealed away in the past but gets released due to Luffy's time - traveling. This force could be something related to the Void Century. It has its own motives to take over the One Piece world and sees Luffy as a major obstacle because he has the potential to disrupt its plans. So it becomes the main antagonist that Luffy has to face in different time periods.
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.
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 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.
One idea could be Luffy travels back in time to the era when Gol D. Roger was still alive. He could learn from Roger about the true nature of the One Piece and gain new insights to use in his own journey. Another could be that he goes back to a time when the Straw Hat crew was just forming and he gets to relive those early days with new knowledge, making different choices to strengthen the crew faster. Maybe he travels to a future time to see the consequences of his actions and then comes back to change things for the better.
Maybe an ancient sea demon that has possessed a pirate captain. This possessed captain is now leading his crew to cause chaos everywhere. They are attacking other pirate ships and even some demigod - related places. Percy has to find a way to exorcise the demon from the captain and stop the crew's rampage. The demon is very cunning and uses the pirate's knowledge of the sea to its advantage.
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.