It could be Orochimaru. In this fanfiction, Orochimaru might hear rumors about the Dragon Balls and their power to grant wishes. Since he is always seeking power and immortality, he decides to hunt for the Dragon Balls. However, because Naruto is so focused on his own battles against Orochimaru in the ninja world, he fails to realize that Orochimaru's new goal involves the Dragon Balls and the entire Dragon Ball Z universe could be at risk.
Maybe a new character created specifically for this fanfiction. This antagonist could be a powerful being from a different dimension who has the ability to manipulate both Naruto's world and the Dragon Ball Z world. He takes advantage of Naruto's neglect of the Dragon Ball Z elements and starts to collect the Dragon Balls for his own evil purposes. He sets traps for both Naruto and the Z - fighters, and because Naruto is not aware of the Dragon Ball Z situation, he unknowingly falls into these traps and makes things more difficult for everyone.
Perhaps in this fanfiction, Naruto is neglected because of a prophecy that foretells of his great power which scares the people in his village. He then stumbles upon a way to enter the Dragon Ball universe. In this new universe, he meets Bulma who is intrigued by his strange powers. With her help, he tries to find a way to either go back to his world and prove his worth or make a new life in the Dragon Ball universe. Along the way, he gets into battles with the likes of Frieza when the tyrant tries to take over a planet that Naruto has come to care about.
Rias herself could be the main antagonist in a way. Since she is the one neglecting Naruto, she stands in the way of Naruto's growth and acceptance in this new setting. Her actions and lack of recognition towards Naruto can be seen as antagonistic.
The main antagonist could be the Sith Lord who oversees Naruto's neglect. This Sith Lord might be so blinded by the traditional Sith ways that he fails to see Naruto's potential, which in turn makes him the main obstacle for Naruto to overcome.
Maybe the main antagonist could be a combination of forces from both worlds. For instance, some dark entity from Zelda's world that followed her to the Naruto world and is using the situation of her being neglected to grow in power. It could be secretly influencing events to cause more chaos and strife in both worlds.
Maybe an evil organization that has its own plans for the Tenseigan. They have been secretly manipulating events to ensure that the Tenseigan remains neglected so that they can steal it and use its power for their own dark purposes. The main character would have to fight against this organization to protect the Tenseigan and its potential for good.
Another possibility is that Alucard himself could become a sort of anti - hero/antagonist. Due to the neglect he faces, he could start to resent the Naruto world and its inhabitants. He might begin to act out, using his powers in ways that are harmful to the people. This would put him at odds with the main Naruto characters who would then have to find a way to either stop him or redeem him.
It could be a new villain created specifically for this fanfiction. Maybe a powerful ninja - like figure from another dimension who is jealous of Naruto's powers and wants to take them for himself while Naruto is in the Batman universe and feeling neglected, so he has to fight this new threat alone at first.
Perhaps there is no traditional 'big bad' antagonist. Instead, the antagonist could be the overall neglect and apathy of the village itself. It's like the village's indifference towards Naruto when he's sick with a cold is the force he has to fight against. He has to break through this wall of neglect to get the care and respect he deserves.
One possible plot could be that in a world where Naruto characters co - exist with Dragon Ball Z characters, Naruto is so focused on his own ninja world problems that he completely overlooks the power and significance of the Dragon Balls. For example, villains from the Naruto world might accidentally stumble upon the Dragon Balls and try to use them without understanding their true power. Meanwhile, Goku and his friends are trying to retrieve the balls from this new, unaware threat.
The Z - fighters like Krillin and Yamcha would be curious about Naruto. Krillin might try to befriend him quickly, while Yamcha might be a bit jealous if Naruto starts getting a lot of attention. In the Naruto world, characters like Sakura and Sasuke might not even notice Naruto's disappearance at first if he has been neglected. But later, they might realize the importance of Naruto when things start to go wrong in their world without him. And in the Dragon Ball universe, Piccolo would be very watchful of Naruto, trying to figure out his motives and if he poses any threat to the safety of the planet.