It could be a group of high - ranking Sith. They consider Naruto as an unimportant being and neglect him. Their collective power and their refusal to accept Naruto as a threat or an asset makes them the main antagonists. They are constantly trying to stop Naruto when he starts to gain power and challenge their authority after being neglected for so long.
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 is a Sith apprentice who is jealous of any attention Naruto might get. So, he makes sure Naruto is neglected. As Naruto starts to rise, this apprentice becomes more and more desperate to stop him, and thus becomes the main force against Naruto in the fanfiction.
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.
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.
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.
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.
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.
It could be the Hidden Leaf Village itself. Since Naruto was neglected there, the village's leadership or some of the villagers who shunned him could be seen as antagonists. They pushed Naruto towards the Akatsuki by not giving him the support he needed.
Maybe an alien race that the Green Lanterns have underestimated. They see Naruto as an easy target since he's being neglected. But Naruto turns out to be more of a challenge than they thought. This alien race could have some sort of power that nullifies the Green Lantern rings, but Naruto's ninja skills are still effective against them.
It could be a member of Naruto's family who is fueling the neglect. Maybe an older relative who believes that the sister has more potential or is more worthy of attention and resources. This person could actively try to keep Naruto down.