It could be a power - hungry shinobi within Kiri. This shinobi might see the Sage as a threat to his own rise in the village hierarchy. So, he uses his influence to keep the Sage neglected and also tries to sabotage any attempts by the Sage to gain recognition.
Perhaps an external enemy from a neighboring village. They sense the potential of the neglected Sage in Kiri and try to manipulate the situation in Kiri to keep him neglected. Their plan could be to later turn the Sage against Kiri or to steal his unique abilities when he is at his weakest point of being neglected.
There could be a secret organization within Kiri itself that wants to maintain the status quo. They believe that the Sage's different way of thinking and potential power could disrupt their control over the village. So, they ensure his neglect and would be the main antagonists trying to stop any positive change for the Sage.
One possible plot development could be that the Sage discovers new powers within himself while being neglected. He might use these powers to prove his worth to the Kiri villagers who overlooked him. For example, he could save the village from a hidden threat, like a powerful and secretive enemy group that the regular shinobi of Kiri were unable to handle.
It could be a young and ambitious Kiri ninja who has grown up seeing the neglect of his village. He might be determined to change the situation and prove that Kiri is not to be underestimated. Maybe he has a special jutsu or ability that he believes can put Kiri back on the map.
It could be a rogue ninja from Kiri who has his own motives for kidnapping Naruto. Maybe he wants to use Naruto's power to take over Kiri. He sees Naruto as a tool to gain control and doesn't care about the consequences for the relations between Konoha and Kiri.
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.
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.