Perhaps a new villain created specifically for this fanfic. A powerful being who has the ability to manipulate both chakra and semblance. This villain could be jealous of the unique bond between Naruto and Neo and wants to destroy it. They would constantly set traps and send minions to attack Naruto and Neo, making them fight for their lives and the safety of their respective universes.
It could be a combination of villains from both universes. For example, Orochimaru from Naruto could team up with Salem from RWBY. Orochimaru is interested in the power of the Grimm and Salem wants to learn about the power of chakra. Their combined evil could be a huge threat to Naruto and Neo, forcing them to use all their skills to defeat this powerful alliance.
It might be a corrupted version of a character from one of the universes. Let's say a RWBY character like Mercury who gets corrupted by the power of the tailed beasts. He becomes power - hungry and wants to rule both the RWBY world and Naruto's world. Naruto and Neo would have to find a way to either cure him or defeat him to restore peace in both universes.
It could be an evil ninja who has somehow gained access to the technology from Neo's world and wants to use it to take over the Naruto world. He might be able to create clones using digital technology, making him a very difficult enemy to defeat.
It could be Darth Sidious. Since he is always looking for power and control in the Star Wars universe, he might see Naruto as a threat to his plans when Naruto arrives in Padme's world. He would try to eliminate Naruto and use Padme as a pawn in his political games.
It could be Ra's al Ghul. He's always interested in things that can give him an edge in his quest for immortality. If he discovers the power of chakra in the Naruto world, he might try to take over both worlds. His skills as a master assassin and his vast resources would pose a huge threat to Naruto and Batman, who would have to put aside their differences to defeat him.
A powerful dark ninja who has made a pact with some dark force from another dimension. He sees Gabriel as an intruder and Naruto as a threat to his plans of taking over the ninja world. He would use his dark jutsu and the power from the other dimension to oppose Naruto and Gabriel, and would stop at nothing to achieve his goals.
It could be Orochimaru from Naruto's world who has found a way to cross into the DC universe. He teams up with some of Batman's villains like the Joker. Orochimaru wants to use the chaos in Gotham to conduct his dark experiments and the Joker just wants to cause mayhem. Batgirl and Naruto would have to deal with Orochimaru's snake - like attacks and the Joker's unpredictable madness.
It could be a powerful ninja from Naruto's world who wants to use Nobunaga's knowledge for evil purposes. This ninja might see Nobunaga as a means to gain more power and control over the ninja clans. He could try to manipulate Nobunaga into starting wars between the clans by using his strategic mind in the wrong way.
The Akatsuki as a whole could be the main antagonist. They might target Naruto as usual, but now with Kabuto on Naruto's side, they have to deal with both of them. The Akatsuki's various members with their unique abilities would pose a great challenge for Kabuto and Naruto to overcome.
One possible plot could be that Naruto somehow gets transported to the RWBY universe. He teams up with Neo. Maybe they start off as rivals, with Neo being distrustful of Naruto at first because of his strange powers. But as they face common enemies, like the Grimm in the RWBY world, they learn to work together and combine their unique abilities, like Naruto's jutsu and Neo's semblance.
It could be an evil ninja from Naruto's world who has somehow gained the powers of a DC super - villain. For instance, Orochimaru could merge with Lex Luthor's intelligence and resources. He would be a formidable foe as he combines Orochimaru's snake - like abilities and knowledge of jutsu with Luthor's strategic mind.
Perhaps an evil ice mage from the Frozen world who has heard of Naruto's power and wants to steal his chakra to become all - powerful. This mage could be jealous of Elsa's natural ice powers and sees Naruto as a means to an end to get rid of her as well.