Madara Uchiha could also be a likely villain. He was very powerful in the Naruto universe with his Sharingan and Rinnegan abilities. He wanted to reshape the world according to his own vision. If he faced the Goku - Naruto fusion, his powerful jutsu and strategic mind would make for an epic battle. The fusion would have to use both Goku's brute strength and Naruto's ninja tactics to defeat him.
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.
It could be an evil Sith Lord who discovers the existence of the Naruto universe and wants to conquer it. He sees Naruto and Ahsoka's alliance as a threat and tries to stop them. This Sith Lord might use his dark side powers to corrupt some of the characters from the Naruto universe and turn them against Naruto and Ahsoka.
It could be Orochimaru. His thirst for power and his willingness to experiment on others would put him at odds with both Naruto and Deadpool. Orochimaru might see Deadpool's regenerative abilities as something to study and Naruto as a threat to his plans. He could try to capture them and use their powers for his own dark purposes.
Kabuto could be a likely villain. He's very intelligent and has a thirst for power. He could use his knowledge of jutsu and his ability to manipulate others to try and steal The Flash's speed force. He might think that by combining it with his own powers and ninja techniques, he could become invincible.
In fanfiction, a Naruto and Goku fusion could be extremely powerful. They both have unique abilities. Naruto has his ninja skills like shadow clones and Rasengan, while Goku has his Super Saiyan forms and Kamehameha. The fusion might combine Naruto's strategic thinking as a ninja with Goku's straightforward combat style. It could result in a character who can quickly assess a situation like Naruto and then attack with overwhelming power like Goku.
Well, it could be super powerful. The fusion might have Goku's Saiyan strength and ability to transform into Super Saiyan forms, combined with Naruto's ninja skills and chakra control. It could fly around with the speed of a Saiyan and use Rasengan - like attacks with the power of a Kamehameha. Just imagine a character with the orange gi and a headband.
It could be Orochimaru. He is always interested in new forms of power and Corrin's unique abilities would attract his attention. He might try to capture Corrin to study her dragon powers and use them for his own evil purposes. Naruto would then have to protect Corrin from Orochimaru's clutches.
I think Zeno would be a really tough opponent. Zeno has the power to erase entire universes, and a Goku and Goku Black fusion, despite being extremely powerful, would have a hard time against such a being with god - like powers.
Goku would be more likely. He is always open to new friendships and challenges. He has a curious nature and would be intrigued by Kefla's power. So he might approach her first to test her strength or just out of friendly curiosity.
Voldemort would still be a very likely villain. He would see the Hulk as a threat or a tool to be used for his own evil purposes. He might try to control the Hulk's mind or use dark magic to make the Hulk do his bidding.
Lex Luthor could be a great villain. He might be jealous of Supergirl's powers and see Flash as an obstacle in his plan to defeat her. He could use his scientific knowledge to create some sort of weapon that targets both speedsters and Kryptonians.