Another option is a being made of pure energy from a dimension beyond the gate. It feeds on chaos and aims to bring chaos to the Naruto world by pitting all the ninja villages against each other.
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.
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.
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.
Maybe another kitsune who has gone bad. In the fanfiction world, there could be a rogue kitsune who sees Naruto as a threat. This antagonist kitsune might be jealous of Naruto's power or his connection to the human world. They could try to undermine Naruto's attempts to protect the village or his friends.
Madara Uchiha would also make a great antagonist. Imagine if he was resurrected and saw Naruto with Samehada as a threat to his plans of creating a new world order. He would use his Sharingan and Rinnegan powers to try and take Samehada from Naruto, believing that with it, he could easily defeat all who oppose him and reshape the ninja world according to his will.
Another possibility is a corrupted dragon spirit that has been awakened due to the mixing of the two worlds. This spirit could be spreading chaos and trying to destroy both the ninja world and the dragon world. Naruto would have to figure out a way to stop it, as it has powers that are beyond what he has faced before.
Perhaps an ancient evil that has been sealed away in the empire for centuries but is released due to the chaos of the crossover. This entity could be more powerful than any foe the Naruto characters have faced before, forcing them to find new ways to fight.
It could be an evil ninja from Naruto's world who somehow gains Kryptonian - like powers. He becomes power - hungry and decides to take over both the Naruto world and Supergirl's world. His knowledge of ninja techniques combined with super strength and other abilities would make him a formidable foe.
A group of rogue shinobi and some of Daria's school bullies could team up. The shinobi would give the bullies some ninja powers, and together they would cause trouble in both worlds. This group would be difficult to deal with as they combine the physical strength of the shinobi with the local knowledge of the bullies.
Maybe an ancient being that was sealed away long ago in the RWBY world but has now been awakened by Naruto's arrival. This being, with its own set of dark powers, sees Naruto as a threat to its plans of domination. It starts to create chaos, summoning Grimm in large numbers and using some form of corrupted chakra - like energy to attack. The RWBY characters and Naruto would have to put aside their differences and combine their skills to defeat this powerful foe.
Madara Uchiha could be an interesting main antagonist in this crossover. Since he already has strong ties to the Sharingan and was a powerful force in the Naruto series. If he somehow got his hands on the Rinne Sharingan's full power, he would be even more formidable. He could use it to manipulate reality or time, making it extremely difficult for Naruto and his friends to stop him.