It could be Orochimaru. He might see the potential in the crow clones and try to manipulate them for his own evil purposes, like using them to carry out his experiments or to infiltrate Konoha.
Madara Uchiha could be an interesting antagonist for a crow clone fanfiction. He might view the crow clones as a new form of power that he can use to reshape the world according to his will, or he could see them as a threat to his plans and try to destroy them.
A possible main antagonist could be a powerful alien who sees Naruto as an abomination. This alien might come from Krypton and believe that Naruto, as a clone of Superman, is a perversion of their species' power. The alien would have all the typical Kryptonian powers but with a more malevolent intent. He would try to destroy Naruto and the Hidden Leaf Village, thinking that he is doing a service to the universe by eliminating this 'false' Superman.
It could be an evil scientist who created the clones for his own malicious purposes. He might want to use their power to take over the Hidden Leaf Village. This antagonist would constantly be trying to control the clones and use them as weapons.
It could be a rogue ninja who has a special ability to disrupt shadow clones. This antagonist might be jealous of Naruto's ability to use shadow clones for training and wants to stop him. Maybe he has a jutsu that can make Naruto's clones go berserk and attack him instead of following his commands.
It could be Orochimaru. He's always been interested in power and new forms of jutsu. Seeing Naruto with Superman - like powers would make him want to either steal those powers for himself or find a way to use Naruto as a tool in his experiments.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Anakin could also face an internal antagonist in the form of his own dark side. The pressures of the Clone Wars, his fear of losing Padmé, and his growing power could all contribute to his inner struggle. This internal battle could be personified as an antagonist that constantly tries to sway him to make wrong choices.
Maybe a new character could be introduced as the main antagonist. This character could be from a hidden village that has been secretly observing Naruto's growth. They realize his potential as a weapon and plan to steal his power or use him to start a war against other villages.
Krampus himself could be the main antagonist. Since he is a figure known for punishing the naughty, his actions in the Naruto world might be seen as unjust. He could be going after ninjas without really understanding their motives, causing a lot of trouble for the main characters.
It could be a rogue ninja who also has somehow acquired bankai - like powers. This antagonist might be jealous of Naruto's newfound abilities and wants to prove that he is the stronger one. So he starts causing chaos in the ninja world, challenging Naruto at every turn.
It could be a rogue ninja who wants to disrupt Naruto's business to gain power. Maybe he's jealous of Naruto's success and popularity in the business world. He could try to steal Naruto's business secrets or sabotage his operations.