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.
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.
Some pure - blood supremacist families who don't approve of their marriage could be antagonists. They might try to cause trouble for Harry and Luna, maybe by spreading false rumors or trying to undermine their work in the wizarding world.
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.
The main antagonists could be some of the more traditional pure - blood families who look down on Ron and Luna's relationship. They might see Luna as an oddity and Ron as not being from a high - enough status family. They could try to interfere with the pregnancy, either by spreading false rumors or trying to separate the couple.
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.