The Akatsuki could also be the main villain in this fanfiction. They learn about the Keyblade and think it could be a powerful weapon to achieve their goals. They start to target Naruto because he has it. Naruto, who has neglected it, now has to quickly figure out how to use it to defend himself and stop the Akatsuki's evil plans.
Maybe Orochimaru. He could sense the power of the Keyblade and wants to take it for himself. He would see Naruto as an easy target to steal it from since Naruto doesn't really understand its value at first.
It could be a new, mysterious character who has the ability to manipulate Keyblade wielders. This villain would target Naruto because he's the main character and the one who has the neglected Keyblade. The villain's goal could be to use the Keyblade to open a portal to a dark dimension and bring chaos to the Naruto world. Since Naruto doesn't know much about the Keyblade, he's at a disadvantage at first. The villain would be very powerful and have minions that are also after the Keyblade.
Well, perhaps Naruto could discover the Keyblade in a hidden realm within the Naruto world. He's neglected it because no one around him knows what it is. Then he has to figure out its powers on his own, like how to use it for combat or to unlock special portals.
It could be Orochimaru. He might have heard about the keyblade and wants it for his own evil purposes. He could try to steal it from Naruto, believing that with the keyblade's power, he could become invincible. Orochimaru is always looking for new sources of power, and the keyblade would be a very tempting addition to his arsenal.
The jailer and an old, wise shinobi could be the main characters. The old shinobi used to be a great hero but now is retired. He sees the same potential in the jailer that he once had. He mentors the jailer, teaching him old techniques that were forgotten. Together, they face a new threat to the village that the other shinobi are ill - equipped to handle.
Maybe an outcast ninja. This person has always been on the fringes of the ninja society. Discovering the neglected sword gives them a chance to prove themselves. They could be someone with a lot of untapped potential who uses the sword to rise above the neglect they've faced.
It could be Samehada itself. Since the story is about it being neglected, it makes sense for it to be the main focus. It could have its own 'voice' and thoughts as it tries to deal with the situation.
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.