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.
Another possibility is that it could be a new character created specifically for this fanfiction. This character could be jealous of Zelda's unique abilities and take advantage of her being neglected to turn others against her. They might spread false rumors about her being a threat, which would further isolate her in the Naruto world.
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 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.
Another possibility is that there is a rogue ninja in Kumo who uses Naruto's neglected state to his advantage. He might try to manipulate Naruto into doing things that would be bad for both Naruto and Kumo, all while remaining in the shadows and making it seem like Naruto is acting on his own accord.
In the 'Naruto neglected Zelda' fanfiction, it could be that Zelda is neglected because the Naruto world is in chaos with its own problems like the Akatsuki threat. The focus is on Naruto and his friends' battles, and Zelda just seems like an outsider. She may have to prove herself by using her abilities in a way that helps the Naruto world, like using her knowledge of puzzles and dungeons to help in a strategic battle.
The elders of Konoha could be the main antagonists. They might be the ones who have been neglecting Naruto all along, and when he leaves, they see him as a threat to Konoha's stability.
The village elders could be the main antagonists. Since they are the ones who decide to neglect Naruto based on the prophecy. They might be so set in their ways and traditional beliefs that they can't see Naruto's potential. They keep him at bay, which causes Naruto to struggle. They are basically the ones creating the main conflict for Naruto in this scenario.