Maybe there could be a mysterious organization that is secretly conducting experiments on Pokémon. Ash and Erika stumble upon their activities during their travels. This organization doesn't want their secrets to be exposed, so they try to stop Ash and Erika from continuing their journey and reporting what they've seen.
A group of rival trainers could be the antagonists. These trainers are jealous of Ash's skills and Erika's knowledge. They constantly try to sabotage their journey, for example, by setting traps or spreading false rumors about dangerous Pokémon in the areas they are about to travel through.
There could be a group of Pokémon poachers who mistake Ash, in his new female form, for an easy target. They might try to capture his Pokémon while he's dealing with the changes in his body and abilities. Or perhaps there's a jealous trainer in Erika's gym who doesn't like the attention Ash is getting, even in his new form, and tries to sabotage his attempts to turn back.
It could be a new evil team that wants to control all the Pokémon for their own greedy purposes.
One possible storyline could be that Ash and Erika are on a journey to find a rare Pokémon that is said to have special powers. Along the way, they face various challenges like rough terrains and other trainers. Another could be that they are traveling to a Pokémon tournament together and during their travels, they help each other improve their Pokémon's skills.
There could be a mysterious dark - type Pokémon that is attracted to the unique energy of the baby. It constantly tries to get close to the baby, which poses a threat to the baby's safety. Ash and Cynthia have to fight this Pokémon off while also trying to figure out why it is so interested in their baby.
A group of rogue scientists who are experimenting on Pokemon in unethical ways could be new antagonists. They might be creating powerful and dangerous hybrid Pokemon.
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.
In some cases, it could be other time - traveling vampires or supernatural beings who have their own agendas. They might not want Bella to interfere with the past as it could disrupt their own plans or power bases. These antagonists could be more shadowy figures, working behind the scenes to thwart Bella's efforts.
It could be that there's a prophecy or a mysterious force at work in Erika's garden. Ash, being his curious self, stumbles upon it and it transforms him. The fanfiction might explore how his Pokémon react to his new form. Some might be confused, while others could be protective. Ash, as a girl, would have to face challenges like different expectations in Pokémon battles and dealing with rivals who see him as an easy target now.
Team Rocket could still be antagonists. Even if Ash goes back in time, they might be up to their old tricks of trying to steal Pokémon. Only this time, Ash has the advantage of knowing their future plans and can thwart them more easily.
Jessie and James are the obvious ones. They are the main members of Team Rocket. Jessie could be constantly trying to outdo Ash in Pokémon battles or contests of skill. James, on the other hand, might be more conflicted about having Ash around. He could secretly admire Ash's kindness towards Pokémon and start to have second thoughts about their Team Rocket activities.