Loki could be a great antagonist. He could use his own time - traveling magic to counter Iron Man's attempts at fixing the timeline. Maybe he wants to create chaos in different time periods for his own amusement or to gain power. Another could be an evil version of Iron Man from an alternate timeline, who doesn't have the same moral compass and wants to take over all timelines.
The Sith could be great antagonists. If Boba Fett travels to a time when the Sith are in power, they would surely see him as an intruder or a potential threat. Their dark side powers and political manipulation would be a huge obstacle for Boba Fett.
It could be a group of rogue ninjas from the new time period who see Jiraiya as a threat to their plans. Since he has different skills and knowledge, they might want to eliminate him.
Another possible antagonist could be Doctor Octopus. His brilliant mind and powerful mechanical arms would give Iron Man and Spider - Man a tough fight. He might be after some technology that Iron Man has or be trying to prove his superiority in the scientific and criminal world, which would bring him into direct conflict with our heroes.
One possible main antagonist could be a dark wizard from the past who senses Hermione's interference in the timeline and tries to stop her. This wizard might be afraid that Hermione's actions will change history in a way that will end his power or influence.
Maybe an ancient and powerful ninja who was sealed away in the past and Team 7's time - traveling disrupts the seal. This ninja then sees Team 7 as a threat to his plans of ruling the world and becomes the antagonist.
In a team Iron Man time travel fanfiction, a great plot could be that Iron Man travels to the future by accident. There, he discovers a world in ruins because of some actions he took in his present. So, he has to travel back and correct those actions. He teams up with his past self and other Avengers from different time periods to make sure the future is saved. This would involve a lot of character development as the different versions of Iron Man and the Avengers have to work together and understand each other's perspectives.
Often, it could be dark wizards from the past who oppose Harry and Amelia's attempts to change things for the better. For instance, a dark wizard who wants to keep a certain evil spell in place that Harry and Amelia are trying to stop.
It might also be time itself. There could be some sort of time - related magic or force that doesn't want the past to be changed. So Harry and Tonks would have to face this 'antagonist' as they try to rewrite history. This could be in the form of time - locked spells or magical barriers that prevent them from interfering in certain events.
It really depends on the specific fanfiction. However, it could be that they travel back to a time when Orochimaru was at his most devious, so he would be a main antagonist. His experiments and thirst for power could pose a great threat to Naruto and Shikamaru's mission in the past.
Often, it could be the same antagonists from the original Naruto series but in a different context. For example, Orochimaru might still be an antagonist if he tries to use the time - travel situation to his advantage, like getting his hands on some ancient forbidden jutsu.