A group of poachers who target Ghost - type Pokemon could be the main antagonists. They might be after Phoebe's strong Ghost - type Pokemon for their own illegal purposes, like selling them on the black market. Another option could be a mad scientist - type character who wants to use Ghost - type Pokemon in some unethical experiments. Or perhaps a powerful, evil trainer who has a vendetta against Phoebe and her Gym, and uses his own strong Pokemon to try and defeat her and take over the Gym.
Another potential rival could be a young prodigy named Lily. She has a diverse team of Pokemon that she has trained from a very young age. Lily is very confident in her abilities and constantly tries to outdo Phoebe in battles. She might also have some unique training methods that Phoebe has to figure out in order to defeat her.
Perhaps a powerful and mysterious trainer. This trainer is jealous of Ash's connection with his Pokemon and his ability to conduct these experiments. He wants to prove that he is the better trainer. So he tries to disrupt Ash's experiments by challenging him to battles at inconvenient times. He also spreads false rumors about Ash's experiments being dangerous to other Pokemon, which causes some local Pokemon communities to be hostile towards Ash.
It could be Team Rocket - style villains who want to capture Naruto because they think he has some special power that can help them control Legendary Pokemon. They might try to trick him or set traps for him.
Another antagonist could be a powerful and corrupted legendary Pokemon. It could be causing chaos in the Pokemon world and Naruto would have to use his skills and the power of his Pokemon team to stop it. This would be a great challenge as legendary Pokemon are extremely powerful, but Naruto has his own set of unique abilities that could give him an edge.
There could also be a trainer who is jealous of Harry's unique abilities, being reborn from the Harry Potter world. This trainer might try to undermine Harry at every turn, stealing his Pokemon or sabotaging his battles, much like Draco Malfoy was often in conflict with Harry in the original Harry Potter series.
Team Flare could be the main antagonists. They might see Baby Callum's connection with Pokemon as a threat to their plans in the XY region. Maybe they try to capture him or his Pokemon to stop him from interfering with their evil schemes.
One common theme is friendship. Phoebe often forms strong bonds with her pokemon and other trainers in the fanfics. Another theme is growth. She usually develops as a trainer, learning new strategies and becoming more confident.
A jealous classmate could be a main antagonist. This person might be envious of Naruto's popularity and his ability to make friends easily. They could try to spread rumors or sabotage Naruto's projects.
The Akatsuki could still be a major antagonist. Even if Naruto is emperor, they might oppose his rule as it goes against their own goals of chaos and obtaining the tailed beasts.
One possible antagonist could be a jealous noble from Naruto's own kingdom who feels that Naruto doesn't deserve the prince title. This person might try to undermine Naruto at every turn, spreading false rumors about him or trying to sabotage his diplomatic efforts.