It could be Frieza. Frieza is a powerful and evil character from Goku's universe. He might see the combined power of Naruto and Goku as a threat and try to eliminate them. He could also be interested in the unique powers that Naruto has, like the Nine - Tailed Fox's chakra, which he might want to use for his own evil purposes.
A new villain created specifically for this fanfic could be the main antagonist. This villain could be a combination of the worst traits from both universes. For example, a being with the ability to steal chakra like Orochimaru and the ability to absorb energy like Cell. This villain would be extremely powerful and would force Naruto and Goku to work together in ways they never thought possible to defeat it.
Madara Uchiha could be a main villain. He is a very powerful and cunning ninja from Naruto's universe. He might view Goku as an obstacle in his plan to reshape the ninja world. He could try to manipulate Goku and Naruto against each other by using his Sharingan abilities. And if he were to get his hands on Goku's power, he could become an even greater threat.
A rogue ninja who has made a pact with dark forces. He wants to use Goku's son to open a portal to the Saiyan planet and then invade it. He would be constantly trying to manipulate the situation to get Goku's son to do his bidding. He has a team of minions who are also skilled in both ninjutsu and some dark form of ki - like powers.
It could be a powerful demon that has the ability to absorb the powers of others. This demon has been observing both Gohan and Naruto from the shadows and wants to take their powers to become invincible.
A new villain could be created specifically for this fanfic. Maybe an interdimensional being that senses the strange energy fluctuations caused by Gohan's training of Naruto. This being, fearing the new power that Naruto might gain, decides to invade Naruto's world to stop the training and take over the world for itself.
A possible main villain could be an evil ninja who has somehow managed to harness dark magic similar to that which the Monkey King once faced. He could be using this magic to try and take over both the ninja world and the world of the Monkey King.
It could be someone like Frieza. Frieza is extremely powerful and evil in the Dragon Ball universe. If he somehow found his way into the Naruto universe or if the fusion character was in the Dragon Ball universe, he would be a great threat. His ability to transform and his cold - blooded nature would make him a tough opponent for the fusion of Goku and Naruto.
One possible plot could be that Naruto and Goku end up in a strange new dimension where they have to live together. They start by trying to understand each other's powers. Naruto is amazed by Goku's Saiyan abilities like the Kamehameha wave, while Goku is intrigued by Naruto's ninjutsu. They then team up to face common enemies in this new world. Maybe there are villains from both their universes that have also been brought there. Together, they train and learn from each other, with Naruto teaching Goku about stealth and strategy, and Goku showing Naruto how to push his physical limits even further.
Well, in this kind of fanfic, it's not so simple to decide who is stronger. Goku's power levels keep increasing exponentially as he reaches new super saiyan forms. He can destroy planets with his power. Naruto, though, has the ability to harness the power of the nine - tailed fox which is also extremely powerful. Moreover, Naruto has his own unique chakra - based attacks. If they were to fight, Goku might start off with an advantage due to his speed and power. But Naruto is a very quick learner and could adapt during the fight. Also, Naruto has his friends and allies that could potentially tip the balance in his favor in a more complex battle scenario.
It's really hard to say. Goku has the power to destroy planets and reach incredible levels of strength with his Super Saiyan forms. However, Naruto has the power of the tailed beasts and his own sage mode which gives him a huge boost in power. And Sonic, while he may not have the raw power like the other two in terms of destruction, his speed is so great that he could potentially outmaneuver both of them. So it really depends on the situation and how the author writes it.
A powerful demon from another dimension could be the main villain. This demon could be seeking to destroy all Saiyans and starts targeting Goku, Caulifla, and Kale. He has unique powers that they have never faced before, like the ability to nullify their energy attacks.
Maybe a powerful demon that has been lurking in the shadows of both universes. This demon is attracted by the unique magic in both Coraline's and Norman's worlds. It starts to possess the people and creatures in both places, and Coraline and Norman must find a way to exorcise it. The demon could be very cunning, disguising itself as friendly beings at first.