Perhaps an evil organization that wants to harness the power of both Naruto and Nero. They might see Naruto's chakra and Nero's Devil Bringer as the keys to ultimate power. This organization could be led by a powerful sorcerer who can manipulate dark magic and has minions from both worlds at his disposal.
A corrupted version of a powerful being from Nero's world could be the main antagonist. Maybe a fallen angel or a demon that has been twisted by dark forces. This being would be a threat not only to Nero's world but also to Naruto's world if it manages to gain enough power. Naruto and Nero would have to put aside their differences and work together to stop this menacing force.
Maybe a new character created specifically for this fanfic. A powerful sorcerer who wants to use Naruto's chakra and Slade's combat expertise for his own evil purposes. He could be manipulating events from the shadows, pitting Naruto and Slade against each other at first until they realize they are being played.
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 Orochimaru. He might be interested in Baby Beel's powers and try to capture him for his own evil experiments. Orochimaru would see Beel as a unique specimen and would stop at nothing to get his hands on him. Naruto would then have to use all his skills and the bond he has with Beel to keep him safe from Orochimaru.
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.
Most likely Danzo would be seen as the main antagonist. His actions throughout the Naruto series were often self - serving and harmful to others, like his role in the Uchiha massacre. So when Naruto talks to him, he would be the one Naruto has to oppose or at least try to change.
Perhaps a rogue ninja from another village who sees Naruto as a threat. This ninja could target Anko and Naruto during their training. He might be jealous of the Hidden Leaf's strength and think that if he can stop Naruto from getting stronger under Anko's teaching, he can weaken the Leaf Village. He could be a skilled fighter with unique abilities that pose a real challenge to Naruto and Anko.
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.
It could be a powerful chef who has been corrupted by the desire for ultimate power in the cooking world. This chef might see Naruto and Alice as threats to his dominance, especially if they start to gain popularity and win Shokugeki battles. He could use underhanded tactics like stealing their recipes or sabotaging their ingredients.