The main antagonist could actually be a group within the village. A cabal of ninja who are jealous of Naruto's potential and the attention he gets from some of the more positive elements in the village. They use their influence to make him feel neglected. When he leaves, they fear that he will expose their actions, so they send assassins after him to keep him quiet.
It could be Danzo. Since he's always been a bit of a shadowy figure in the Naruto world, he might be the one behind Naruto's neglect in the village. He could have spread rumors or influenced others to keep Naruto down, and when Naruto leaves, he might send agents to stop him from becoming a threat outside the village.
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.
In this fanfiction, Naruto might be neglected not just by the villagers but also by some of his so - called friends. This heartbreak makes him leave. He then travels to different lands. Along the way, he meets an old hermit who teaches him ancient ninja techniques that are long forgotten in his village. With these new skills, he contemplates whether to return to the village and show them what they missed out on or to start a new life away from the place that has caused him so much pain.
It could be a rogue Anbu member. This person might be jealous of Naruto's power and popularity within the Anbu. So, they spread false rumors about Naruto which lead to his decision to leave the village. This antagonist would then try to further harm Naruto while he's outside the village, using their own Anbu skills against him.
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.