A powerful dark wizard could be the main antagonist. He might be jealous of the dragon rider's powers and the bond with the dragon, and wants to break that bond and steal the rider's powers for himself.
It could be a powerful dragon hunter. This person would see Naruto's dragon as a prize to be captured or killed. They might have a personal vendetta against dragon riders in general.
It could be a dark wizard who wants to control the dragons for his own evil purposes. He might see Harry as a threat because Harry is forming a bond with the dragons and teaching them to resist dark magic.
It could be Orochimaru. He is always seeking power and the strange and powerful abilities of the Ghost Rider might be something he desires. He could try to capture or study the Ghost Rider to gain an edge in his own plans for power and immortality.
Perhaps a powerful sorcerer who wants to capture the black horse for his own dark purposes.
It could be a former ally of the Pokemon Master who has turned evil. Maybe they felt overshadowed by the Pokemon Master and now seek revenge. For example, they might have found a dark artifact that corrupts them and gives them the power to control other trainers' Pokemon.
A good antagonist could be a character from the 'Resident Evil' universe, like Albert Wesker. His superhuman abilities and evil plans for global domination would pose a huge threat to Alex Rider. Alex would have to use his wits and skills to stop Wesker's bio - terrorist plans.
It could be a powerful and shadowy figure from Wolf's past, like an old military commander who has gone rogue. This person might have a vendetta against Wolf for some past betrayal and sees Alex as a way to get to Wolf, using Alex's importance in the spy world as leverage.
A powerful dark wizard from the human world who has found a way to cross over into Equestria. He wants to harness the magic of the Elements of Harmony to increase his own power. He sees the Ghost Rider as a threat to his plans and tries to eliminate him while also causing chaos in Equestria.
A group of dark magic - using reindeer could be the main antagonists. Maybe they were banished long ago for misusing their magic, and now they've returned. They target Santa Baby because they know she's important to Santa and the whole Christmas operation. They try to steal her magic to make themselves powerful enough to take over the North Pole.
It could be a rogue ninja who took advantage of the chaos during the war. This ninja might have been gathering power in the shadows and now sees Naruto as a threat to his plans.