The dark mages of that time could be antagonists. They might sense Shirou's different magical energy and try to either control him or destroy him. Also, there could be traitors within Arthoria's court who don't like the idea of an outsider like Shirou being around and causing changes, so they work against him.
One idea could be Shirou trying to learn the ways of chivalry from Arthoria. He might struggle to adapt to the different moral and ethical codes of that time. Another could be Shirou using his modern knowledge to help Arthoria in battles, like devising new strategies.
A powerful rogue Soul Reaper could be an antagonist. This Soul Reaper might be jealous of Ichigo's new - found time - control ability and try to steal it for his own dark purposes. Maybe he wants to use it to rewrite history in his favor, eliminating all those who opposed him in the past. Another potential antagonist could be an ancient and evil entity that has been trapped in a time - locked dimension. Ichigo's use of time - control accidentally releases this entity, and it now wants to use Ichigo's power to break free completely and wreak havoc on the world. There could also be a group of Quincy who see Ichigo's power as a threat to their own plans of taking over the spiritual world. They try to stop him from using his time - control ability by any means necessary.
Danzo could be a potential antagonist. Even in the past, he might be plotting against the Uchiha clan. If Sasuke and Hinata try to change things related to the Uchiha, Danzo could see them as a threat and try to stop them.
One potential antagonist could be Orochimaru. If Naruto and Temari travel back to a time when Orochimaru was at the height of his power and evil plans, he would surely oppose them. He might see their knowledge of the future as a threat to his schemes to gain immortality and power over the ninja world.
One potential antagonist could be a rogue ninja who also has aerokinesis but uses it for evil. He might be jealous of Naruto's natural talent and try to undermine him at every turn. Another could be a powerful sorcerer from a far - off land who has come to the Naruto universe specifically to find someone with aerokinesis to either steal their power or use them as a tool. There could also be a group of anti - ninja who see Naruto's new power as a threat to their plans of overthrowing the ninja system and they try to eliminate him.
A jealous courtier could be an antagonist. Maybe someone in the princess's own court who is envious of her position and tries to stop her time - travel adventures out of spite or to gain power for themselves.
Perhaps Orochimaru could still be an antagonist. In this fanfiction, he might be jealous of Naruto's new god - like gaming powers and try to steal them for his own experiments.
There could be a jealous fellow ninja from within the village who feels that Naruto is getting too much attention for his blade - mastery. This ninja could turn against Naruto and become an antagonist, perhaps even teaming up with external forces. Also, an ancient evil entity that was sealed away long ago might be awakened by the power of Naruto's blade and seek to destroy him and the village to regain its freedom.
It could be some of the hospital's board members who might not approve of their relationship and Cameron's pregnancy while working at the hospital. They could try to make things difficult for the couple.
Well, there could be an evil scientist in the fanfiction. This scientist might be researching the power of hypnosis on Pokemon trainers and sees Iris as a perfect test subject. They would use their advanced technology and knowledge of Pokemon behavior to hypnotize her. Also, a powerful psychic - type Pokemon that has gone rogue could be an antagonist. It might hypnotize Iris to do its bidding, like stealing other powerful Pokemon or causing chaos in Pokemon battles. And don't forget about a group of treasure hunters who want to use Iris's hypnotized state to find a hidden treasure that only she knows the location of through her adventures.