A new villain created specifically for this fanfiction could be the main antagonist. This villain could be a sorcerer who has found a way to combine the magic of the DC universe with the chakra system of Naruto's world. He wants to use this power to rule both universes and Naruto and Wonder Woman must stop him.
It could be Darkseid. He might see Naruto as an unknown variable in the DC universe and want to either control his power or eliminate him. His forces could also be a threat to Wonder Woman's world, so they have to team up to stop him.
One possible plot for a 'naruto x wonder women dc new 52 fanfiction' might involve Naruto being mistaken for a new metahuman in the DC universe. Wonder Woman takes him under her wing to figure out his powers. Along the way, they discover that Naruto's willpower is as strong as any Amazon's. They then have to face a threat that is using some sort of dark magic that Naruto has some knowledge about from his own world, and they use their combined knowledge and abilities to defeat it.
It could be an evil ninja from Naruto's world who has somehow gained the powers of a DC super - villain. For instance, Orochimaru could merge with Lex Luthor's intelligence and resources. He would be a formidable foe as he combines Orochimaru's snake - like abilities and knowledge of jutsu with Luthor's strategic mind.
The Green Goblin could also fit well. He could form an alliance with some of Wonder Woman's foes. His chaotic nature and love for destruction would contrast with the heroes' quest for peace. He could target both of them, trying to break their partnership and cause mayhem in the city.
Maybe it's an ancient evil entity that has been awakened by the combined power of Naruto's chakra and Wonder Woman's divine energy. This entity sees them as a threat to its plan of ruling both universes and thus tries to eliminate Wonder Woman first, which is when Naruto steps in to save her.
It could be Kaguya Otsutsuki. Since she has powerful abilities and a thirst for power, she would see Kefla's power as a threat and Naruto's influence as something to be eliminated. She might try to manipulate events to turn the ninja world against Kefla and Naruto.
It could be someone who wants to merge their two worlds in a chaotic way. Maybe an evil scientist from Leela's world who has discovered the power of chakra and wants to use it for his own dark purposes. He could try to capture Naruto to study his chakra and use it to take over both universes.
The main antagonist could be an evil merman who wants to take over Ariel's kingdom and is also jealous of her friendship with Naruto. He might use his dark water - based magic to try and stop them.
An ancient evil force that was sealed away by Hashirama long ago could be released in Naruto's time. This entity, having a grudge against Hashirama for imprisoning it, would see Naruto as an obstacle too since he's allied with Hashirama. It could have powers that are completely unknown to the modern ninja world.
It could be Salem herself if the fanfiction focuses on Naruto trying to stop her evil plans. Since Salem has a long history of causing chaos and destruction, Naruto would see her as a force to be reckoned with and try to oppose her.
It could be a rogue ninja from an old clan who has a vendetta against both Konoha and Kumogakure. This ninja has been gathering power in secret and plans to destroy both villages to avenge his clan's past defeat at the hands of the combined forces of the two villages.