A powerful dark dragon could be the main antagonist. This dragon might be jealous of the little flame dragon's unique abilities or position within the dragon community. It could constantly try to undermine the little flame dragon and cause trouble for it.
A group of dragon hunters could serve as the main antagonists. They see the little flame dragon as a valuable trophy or a source of rare materials. They might use all kinds of traps and weapons to try and capture the dragon, and the little flame dragon has to outwit them at every turn to stay alive.
An evil wizard who wants to capture the little flame dragon for its magical essence could be the main bad guy. He might plan to use the dragon's essence to increase his own power and control over the land. The wizard could send his minions to hunt the little flame dragon down.
It could be a powerful dark wizard who wants to control the dragons and sees Naruto as a threat because of his newfound dragon - trained powers.
It could be a dark wizard who wants to use the dragons for evil purposes. He might try to control them and make them attack Hogwarts or other wizarding communities.
The Trix could be the main antagonists. They've always been after power and Bloom's dragon flame is a great source of power. They would stop at nothing to get their hands on it and use it for their own evil plans.
It could be a human fisherman who has discovered a way to capture mermaids and is hunting them down for their valuable scales and tails. Aquata has to stop him before he wipes out all the mermaids in the area. Or perhaps an ancient sea monster that has been awakened from a long slumber and is causing chaos in the ocean, and Aquata is the only one brave enough to face it. This sea monster could be very difficult to defeat as it has powers that are unknown to the mermaids.
A sea witch could be a great antagonist. She might be jealous of Attina's beauty and grace, and try to use her magic to turn Attina into an ordinary fish. The sea witch could also create all sorts of obstacles for Attina and her friends, like summoning sea monsters or causing storms.
A powerful sea witch who is jealous of Marina's beauty and popularity among the mermaids could be the main antagonist. She might try to steal Marina's voice or tail to make her powerless.
Maybe an enemy spy who has infiltrated the little soldier's unit. This spy would be constantly trying to undermine the unit's operations and would be a constant threat to the little soldier and his comrades. He could be very sneaky and hard to detect, which would make him a formidable antagonist.
It could be an old, grumpy neighbor who is constantly annoyed by the eight little hellions' antics. He tries to get them in trouble at every turn and devises all sorts of plans to make their lives miserable.
An ancient dragon that has turned evil due to some dark magic could be the main antagonist. This dragon might see Natsu as a threat because of his unique combination of powers and wants to eliminate him. Natsu would then have to use all his skills and the help of his friends to fight this dragon. The dragon could also have minions that are constantly causing trouble for Natsu and his guild.
Maybe there's an evil spirit that has a grudge against the dragons. When the sister starts to get involved with the dragons, this spirit targets her. It could be a spirit that was once wronged by the dragons in the past and now wants revenge, not caring that the sister is just a new acquaintance to the dragons.