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.
Perhaps an evil scientist who has been experimenting with time travel and has created powerful bio - mechanical creatures. These creatures start attacking the cities, and Goten and Future Trunks have to stop them and the scientist behind it all. The scientist believes that by creating chaos, he can reshape the world according to his own vision.
One possible plot could be that Goten and Future Trunks meet during a time - traveling accident. They initially have some misunderstandings due to their different upbringings and experiences. But as they start to train together, they learn from each other's fighting styles and develop a deep friendship. They then team up to face a new, powerful enemy that threatens both their timelines.
It could be Frieza. Since he has a long - standing enmity with the Saiyans. His presence would create a great threat that King Vegeta and Trunks would have to overcome together. King Vegeta has his own history with Frieza, and Trunks knows how powerful Frieza can be in the future.
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.
The androids could still be the main antagonists. Even if they have been defeated in some timelines, in a fanfiction, they could be brought back stronger or with new abilities. Their cold and ruthless nature would make them a great challenge for Gohan and Trunks to overcome.
Cell could still be a great antagonist. Imagine a scenario where in the fanfiction, Cell follows Future Trunks through time. He then starts to absorb different beings in the new timeline in a more devious way than in the original story.
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.
Well, in the world of fanfiction, the possibilities are endless. Goten and Trunks are popular characters, and while not all fanfictions will feature them kissing, there are likely some that do. It really depends on the creativity and interests of the fanfiction authors. Some might write it in a more innocent, platonic way, while others could be more romantic. You have to dig through the vast collection of fanfictions to find the ones that match what you're looking for.
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.
Perhaps there is no traditional antagonist. Instead, the conflict could be within Percy himself. His future self might have some dark secrets or regrets that Percy in the present doesn't want to face. So, in a sense, Percy's own denial or fear could be the 'antagonist' in this fanfiction.
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.