A future version of Mega Man himself could be the antagonist. Maybe in the future, something goes wrong and Mega Man becomes corrupted. He then travels back in time to stop his past self from becoming the hero he is supposed to be, in order to maintain his own corrupted existence.
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 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.
Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.
It could be a dark wizard from the past who has the power to manipulate time. This wizard might see Natsu and Mira as threats to his plans to change the past for his own evil gains. He would try to stop them from interfering with his time - related schemes.