Voldemort's remaining followers could be her enemies. They might be planning something new and Hermione, as a spy, would be trying to stop them. Also, some corrupt Ministry of Magic officials who are up to no good. They would see Hermione as a threat to their secret operations.
Well, there could be a group of rogue wizards who are trying to steal powerful magical artifacts. Hermione, as a spy, is on their trail. They would see her as an enemy because she is trying to thwart their plans. Another potential enemy could be a powerful dark wizard who has returned and is trying to take over the wizarding world. Hermione's spying efforts would be focused on gathering information about this wizard and his followers in order to stop them.
In these fanfictions, her enemies could be other students who are jealous of her or who have their own dark motives. For example, a power - hungry student who wants to use dark magic and Hermione is in the way of their plans. And then there are the Death Eaters' sympathizers who are still lurking in the shadows. They would do anything to keep Hermione from uncovering their secrets and bringing them to justice.
A new dark wizard could rise. This wizard might be jealous of the fame and power that Harry has, and seeing his daughter as an extension of that, decides to target her. Maybe this new dark wizard is seeking to gain control over the wizarding world and sees her as a key obstacle in his path.
The Titans could be potential enemies. Even though they've been defeated before, some of them might be resentful and see Percy as the Chaos Champion as a new threat to their possible plans of a comeback. Kronos, for example, might have some of his essence lingering and try to possess other powerful beings to go against Percy.
The First Order could still be a threat. They might see her as a symbol of the Resistance and try to eliminate her. Or it could be a new Sith cult that has risen in the ashes of the old Sith order.
For allies, All Might could be an interesting choice even when they are babies. All Might might sense Izuku's potential and also see that Shigaraki could be redeemed if guided right. Another potential ally could be Aizawa. He could be the one who trains them in basic self - defense skills when they are kids. As for enemies, the League of Villains could be a problem for Izuku, as they might see him as a threat to their plans with Shigaraki. Also, some of the more evil - minded heroes who don't believe in second chances for villains like Shigaraki could be enemies.
There could be a new dark wizard or witch who is jealous of the Potter family's legacy. They might target Harry Potter's daughter to try and bring down the family name and prove their own power.
The Death Eaters could still be a major threat. Even with Voldemort gone, some of them might be trying to revive the dark ways and see the wizard king as a big obstacle in their path.
The children of Ares might see Percy as a threat. Since Cupid represents love and Ares represents war, their natures are quite opposite. The Ares kids could be jealous of Percy's powers or simply not trust him because of his different lineage.
The traditional enemies of the demigods, like the Titans or the Giants, could still be his enemies. They might see him as an abomination because of his father being Charon. Also, some of the more puritanical demigods who follow the Olympian gods strictly might oppose him.
The Akatsuki could be potential enemies. They might see Naruto's little sister as a way to get to Naruto. Maybe they think they can use her as a hostage or extract some information from her about Naruto or the Nine - Tails. Another enemy could be some of the rogue ninja who are after the bounty on Naruto's head and see his sister as an easy target to get to him.
The Titans could still be a threat. Even though they were mostly defeated, there could be some remnants or new Titans emerging. For example, a Titan who was in hiding and now sees Percy as a threat to his plans of taking over again.