The Kingpin could be an interesting antagonist in a more street - level crossover. Imagine a crossover with Daredevil's world. The Kingpin, with his criminal empire, could try to use Ghost Rider's power for his own evil purposes. He might try to find a way to control Ghost Rider, not realizing the danger he's getting himself into.
Dormammu could also be a formidable antagonist. His dark magic and his desire to expand his dark dimension could put him in conflict with Ghost Rider. If there's a crossover with the Fantastic Four world, he could use his powers to try and take over Earth while Ghost Rider tries to stop him, and the Fantastic Four might get caught in the middle.
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.
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.
It could be a powerful devil who sees the Ghost Rider as a threat to his plans in the school. Maybe this devil wants to take over the school or gain more power among the students, and the Ghost Rider's presence and his sense of justice stand in the way.
In terms of anime characters, Ichigo Kurosaki from 'Bleach' could be an interesting addition. His ability to see and fight spirits could be related to Kiva's battles with Fangires. They could end up in each other's worlds and have to learn to use their powers together to fight off both Hollows and Fangires.
Another possibility is Kamen Rider Decade. Decade has the ability to transform into different Kamen Riders, and his presence in a crossover with Kickhopper could bring a lot of different elements into the story. He could use his powers to help Kickhopper access new forms or abilities, or they could travel through different Kamen Rider worlds together to stop a multiverse - level threat.
One great Vampire Knight and Ghost Rider crossover fanfic might be titled 'The Night Riders of Cross Academy'. In this fic, the dark and brooding world of Vampire Knight meets the hellish and vengeful world of Ghost Rider. The main character, perhaps Zero, could gain the powers of Ghost Rider, adding a whole new level of badassery to his fight against the vampires at Cross Academy. It could explore how his new powers affect his relationships with Yuki and the other characters.
Well, one possibility could be that Ghost Rider's hellfire powers somehow interact with the Transformers' technology. Maybe his fire could be used to supercharge a Transformer's weapon or power source. For example, if Optimus Prime were to team up with Ghost Rider, Prime could use the enhanced power to defeat a more powerful Decepticon.
A powerful rogue Shinigami who has turned against Soul Society and is seeking to use Mugetsu Ichigo's power for his own evil purposes. This antagonist could have some dark secrets related to Ichigo's past or his family, which would add more depth to the story.
Dr. Doofenshmirtz from Phineas and Ferb would be a great antagonist. He could cross over into Jimmy's world and try to steal Jimmy's inventions to use in his own evil plans. His wacky schemes would clash with Jimmy's scientific logic, creating a lot of comical and action - filled situations.
It could be a power - hungry noble from the imperial court who sees Naruto as a threat to his own ambitions of ruling. This noble might have his own group of skilled fighters and use underhanded tactics to try and undermine Naruto's rule as emperor.