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.
In some cases, it might be the Ministry of Magic from the past. They might see Harry and Amelia as threats to the stability of the magical world as it was then. Maybe they are trying to enforce old, unjust laws and Harry and Amelia are fighting against that. They have to outwit the Ministry officials who are using all their resources to stop them.
There could also be a group of powerful magical creatures who are against the idea of Harry and Amelia interfering with time. These creatures might have their own reasons for wanting the past to remain unchanged, like protecting their habitats or a certain way of life that they fear will be disrupted if Harry and Amelia succeed in their time - traveling mission.
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.
In some cases, time itself or the consequences of changing time could be seen as an antagonist. For example, if they try to change a major event, they might face unforeseen consequences like creating new threats or endangering the future they came from. So, in a sense, the very fabric of time and its rules could be working against them.
The obvious antagonists would be the Death Eaters. They are always up for causing chaos and harm. If Voldemort has a particular interest in Amelia Bones, perhaps because of her knowledge or position in the wizarding world, he would send his loyal Death Eaters to capture her. Another possibility could be some rogue dark wizards who are trying to gain power and see Amelia as an obstacle.
Bellatrix Lestrange could also be a common antagonist. She was extremely loyal to Voldemort and very powerful. If Harry and Hermione's actions in the past disrupt the Death Eaters' plans, she would surely oppose them.
There could be time - traveling dark wizards who oppose Harry and Hermione's attempts to fix things in the past. These wizards might have their own agendas for the past and present, and see Harry and Hermione as threats to their plans. They could use dark magic to try and stop them or even manipulate time against them.
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.
It could be some of the historical villains from Naruto's past that were thought to be long gone but are now resurfacing due to the time travel. For example, Madara Uchiha might be an antagonist if they travel back to a time when he was still active and plotting against Konoha.
Often, Aizen can still be a major antagonist even in time travel fanfictions. His schemes might extend across time, and Ichigo and Orihime have to figure out how to stop his plans that are messing with different timelines. Another could be the more powerful versions of Hollows from different time periods. They might be stronger and more menacing than the ones Ichigo and Orihime are used to in their original timeline.
It could be the same antagonists from the original Naruto series, like Orochimaru or Madara Uchiha. Since Naruto and Temari are time - traveling, they might encounter a younger version of these villains at a time when they were just starting their evil plans. Another possibility is that they create new antagonists by changing the past in some way. For example, if they prevent a certain character from dying, that character could turn out to be an antagonist in the altered timeline.