Perhaps a dark wizard who has found a way to control mermaids. He wants to use Lucy as a weapon against the Fairy Tail guild. He may have some vendetta against the guild and thinks that by turning Lucy into a mermaid and controlling her, he can get his revenge. He would be very cunning and use all sorts of dark magic to try and achieve his goals.
A merman who wants to take over the mermaid kingdom and sees Lucy as a threat. Since she has ties to both the land (through Fairy Tail) and the sea (as a mermaid in the fanfic), he might think she'll stop his plans for domination. He could be very powerful and have an army of sea creatures under his command. He'd constantly be sending his minions to attack Lucy and her friends.
It could be an evil sea witch. She might be jealous of Lucy's newfound mermaid powers or her connection to the Fairy Tail guild. The sea witch could try to steal Lucy's powers or use her to gain access to the land world.
It could be a new character introduced specifically for the fanfiction. Maybe a powerful mage who has a vendetta against Lucy and somehow manages to drive her out of Fairy Tail by causing trouble for her within the guild.
A powerful magical being from another dimension could be the main antagonist. This being senses the departure of Lucy and Juvia from Fairy Tail and sees it as an opportunity to invade their world. It tries to stop the two girls from getting help or finding a way to stop it, as they are two of the most powerful mages outside of the guild protection now.
The main antagonist could be a powerful and ancient fairy who has been banished long ago but now returns to seek revenge on the fairy world. And Lucy, being a new and important part of the fairy world, becomes a target. This antagonist might have unique and dark magic that makes it extremely difficult for Lucy to defeat. Also, the antagonist could have some sort of grudge against the fairy queen or king, and Lucy is caught in the middle of this power struggle.
It could be a rogue Dragon Slayer who is jealous of Lucy's new - found powers. This character might have been exiled from their own guild for misusing their powers and now sees Lucy as an easy target to prove their superiority.
It could be a former Fairy Tail member who turned to the gangster life. They know all the guild's secrets and weaknesses, so they can be a very formidable opponent. They might have left the guild because they felt betrayed or didn't get the recognition they thought they deserved.
It could be an ancient dragon that has been awakened from a long slumber. This dragon might have a vendetta against Ignia or the Fairy Tail guild for some past transgression.
A group of rogue mages who oppose the idea of Yukino joining Fairy Tail. They might view Fairy Tail as a threat to their own plans in the magical world. They target Yukino as the 'newcomer' in the guild, thinking that if they can get rid of her, they can weaken Fairy Tail. They use various underhanded tactics like spreading false rumors about Yukino within the guild and attacking her when she is on solo missions.
It could be Natsu. He's hot - headed and might not understand Naruto's ways at first. He could see Naruto as a threat to his position in the Fairy Tail guild and start bullying him to assert his dominance.
It could be Zeref. Since he has a complex relationship with Natsu in the original story, he might manipulate things behind the scenes to make the Fairy Tail guild betray Natsu. Maybe he wants to isolate Natsu for his own evil plans.
Zeref could be a great main antagonist. His long - standing connection to dark magic and his complex relationship with the Fairy Tail characters make him a powerful and menacing figure. He could be the one orchestrating the universal war in an attempt to finally achieve his dark goals.