The Diamonds could also serve as antagonists in a different way. Even though they've changed, there could be some old beliefs or grudges that resurface when the past and future collide. For instance, they might try to re - assert their old authority in the face of the new, more equal future.
It could be a corrupted Gem from the past that was somehow locked away and now resurfaces in the future, angry at the changes that have occurred. This Gem might not understand the new world order and wants to return things to how they were.
Perhaps past versions of the Crystal Gems meet their future selves. They could be shocked by how much they've changed, or they might learn valuable lessons from each other. The past Gems could see how their actions in the past led to the future they now inhabit, which could be a really interesting exploration of cause and effect.
It could be a new villain from the future that somehow follows future Gohan back in time. This villain might be an evolved form of an existing enemy, stronger and more cunning. They could be after the secrets that future Gohan holds about the future technology or the power levels of the Z - fighters in the future.
It could be another gem who doesn't want Steven and White Diamond to form an alliance. Maybe a rogue gem who fears that their combined power would disrupt the current power balance in the gem universe.
A group of Homeworld Gems who believe that Black Pearl has become too 'contaminated' by her interactions with the Crystal Gems and Steven. They see her as a threat to the traditional Gem order and send a special task force to capture or destroy her, which would make them the main antagonists as they try to stop Black Pearl from living her new life.
Another option is an ancient evil that was once sealed away by the Diamonds long ago. But due to some recent events in the Steven Universe universe, it is starting to break free. This evil force could target Blue Diamond because of her past actions and Steven because of his potential to stop it.
In 'Steven Universe Watch the Future fanfiction', Steven is bound to be a central figure. He's the protagonist of the original series, after all. Alongside him, the Crystal Gems - Garnet, Amethyst, and Pearl - are very likely to be main characters. They've been with Steven through thick and thin. Additionally, characters like Peridot, Lapis Lazuli, and Bismuth, who have become important parts of Steven's life in the later parts of the series, could also be main characters. Connie, with her connection to Steven and her own growth in the story, is also a strong candidate for a main character.
If it was a crossover with "She - Ra and the Princesses of Power", Adora could be a main character. Her strong leadership and the power of She - Ra would be an interesting contrast to Steven's more laid - back leadership style. Together, they could fight against a common enemy that threatens both their worlds.
It could be a corrupted Gem that has the ability to disrupt Steven's new ways of sensing the world. This Gem might be able to create illusions that confuse Steven's other senses, making it difficult for him to rely on his friends or his new powers.
Another possibility is that a new villain emerges as a result of the time - travel or whatever mechanism brings future Deku to the present. This villain could be from a future where Deku's actions (or inactions) have led to a more dangerous world, and he travels back in time to stop Deku from making those mistakes again. However, his methods are extreme and dangerous, making him the antagonist of the story.
It could be a rogue Saiyan from an alternate timeline who has come to their universe to prove his supremacy. He is jealous of the power that Goten and Future Trunks possess and wants to take it for himself.