It could be an ancient evil that has been awakened by Naruto's newfound power. Maybe a dark spirit that was sealed away long ago and now wants to use Naruto's mega evolution energy for its own evil purposes.
In a 'naruto mega evolution fanfiction', the plot might revolve around Naruto's friends also being affected by this concept of mega evolution. For instance, Sasuke could develop a new form that is a combination of his Sharingan and some external force. This could lead to new rivalries and alliances as they all adapt to their new powers. It could also involve Naruto having to master his new form, which might come with some uncontrollable aspects at first.
Dr. Wily would be a very likely main antagonist. He could be using time travel to his advantage, for example, going back in time to steal important technology before Dr. Light discovers it. This would give him an even greater edge in his evil plans in the present or future.
It could be an all - seeing, all - controlling AI. This AI might view Mega Man as a disruption to its perfectly ordered future world. It would use its army of highly advanced robots to try and eliminate Mega Man before he can change the future in any way.
Well, it could still be Dr. Wily. He might see Mega Man's transformation as an opportunity to finally defeat him. Since Mega Man is in a new and potentially vulnerable state, Dr. Wily could try to take advantage of that. He might even have some new schemes that are designed to specifically target a female - bodied Mega Man.
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.
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.
It could be a rogue Kumo ninja who is jealous of Naruto's power and wants to prove himself by defeating Naruto. This ninja might have some dark secrets and a grudge against Kumo as well.