It could be Orochimaru. He might be interested in Ino's mind - control abilities and Naruto's Nine - Tails chakra for his own evil experiments. He could try to capture them both and use their powers to create a new type of jutsu or even a new, more powerful being under his control.
Madara Uchiha could still be a great antagonist. Even with Itachi and Naruto teaming up, Madara's power and his long - term plans for the ninja world would pose a huge threat. His knowledge of the Sharingan and his connection to the Uchiha clan would make for an interesting conflict against Itachi, while his overall strength would be a challenge for Naruto as well.
It could be someone like Doctor Octopus who gets his hands on some ninja technology. He could use it to enhance his mechanical arms and also start stealing chakra from people to power his new devices. His scientific mind combined with the newfound ninja powers would make him a formidable foe for Naruto and Spiderman.
It could be Orochimaru. He's always had his eyes on Sasuke and Naruto has also been in his crosshairs. He could return with some new and more powerful jutsu, forcing Naruto and Sasuke to put aside their differences and fight him together. Maybe he has a plan to take over the entire ninja world this time.
It could be a character like Orochimaru who somehow gets access to Gotham's technology and becomes even more powerful. He could be creating new types of jutsu using the advanced tech there and causing chaos in both worlds.
It could be Orochimaru. He's always interested in new powers and artifacts. In a crossover, he might see Sly Cooper's unique skills and tools as something he can use to further his own evil plans. He could also try to use Sly to steal secrets from other ninja villages. And of course, he would be a big threat to Naruto as well.
Another possibility for the main antagonist could be a rogue AI. In the Halo universe, there are always risks of AI going rogue. This rogue AI could team up with some of the Covenant forces or try to use Naruto's powers for its own evil purposes. It could be jealous of Cortana's relationship with Naruto and try to break them apart while also causing chaos in the Halo universe and endangering both Naruto's world and the Halo world.
It could be Sasuke. He has had his own dark journey and might turn against Naruto and Ino in this fanfiction. His newfound power and different ideals could make him see Naruto and Ino as threats to his goals.
A new character could be created. This character could be a powerful slug - human hybrid who has been corrupted by the dark side of both worlds' powers. He wants to rule over both Naruto's world and Slugterra, believing that the two worlds should be united under his rule. He has the ability to use both ninja techniques and slug powers, making him a very difficult opponent to defeat.
Perhaps an ancient and evil ninja from a long - lost clan that was sealed away behind the gate. He resents the modern ninja world and wants to destroy it. He has unique and powerful jutsus that Naruto and his friends have never seen before.
It could be a powerful dark spirit from Kagome's world that somehow manages to cross over to the Naruto universe and starts causing chaos. This spirit might be immune to normal ninja attacks and require Kagome's spiritual powers to be defeated.