The fanfiction could center around an alternate universe where Sasuke and Sakura are the main focus instead of Naruto. In this Experiment 101, they are trying to find a way to bring peace to their village in a completely different way. They might start by reforming the ninja education system. They face opposition from the traditionalists but manage to make some changes that could potentially change the future of their village for the better.
One possible plot could be that in 'experiment 101', Orochimaru creates a new type of clone of Naruto. This clone has all of Naruto's powers but also some unexpected abilities. Maybe it can control a new type of chakra that Orochimaru infused during the experiment. And Naruto has to face this clone in a battle that not only tests his physical strength but also his mental resolve as he sees a version of himself being used for evil.
In this fanfiction, Sasuke may start to see the value of teamwork in a new light. Experiment 101 could put him in situations where he has to rely on Sakura and others more than he ever has before. This would make him less of a lone wolf. Sakura would develop her combat skills further. She might learn some new fighting techniques from Sasuke or from the experiment itself, and this would change how she is perceived in the ninja world. Also, their relationship would develop into a more equal partnership.
Well, it could be about Ash experimenting with new battle strategies. For example, he might try to combine different Pokemon moves in unexpected ways. Maybe he'd experiment with training his Pokemon in unique environments like a mysterious forest filled with rare Pokemon. This could lead to his Pokemon evolving in new and exciting ways, and he could discover new Pokemon abilities along the way.
Another possibility is that the main villain could be a spirit or entity that has been trapped for centuries. It uses its influence to make the Hidden Leaf Village conduct 'experiment 101' on Naruto. The spirit hopes to use Naruto's body as a vessel to be reborn into the world and wreak havoc. So it manipulates the events and people involved in the experiment from the shadows.
Perhaps Orochimaru's experiment accidentally releases an ancient evil that was sealed long ago. Naruto, being the hero he is, takes it upon himself to reseal the evil. Along the way, he discovers secrets about his own family and the origin of chakra that are linked to Orochimaru's experiment.
A simple plot could be that Sakura gets pregnant and Sasuke is overjoyed. They start making plans for their future in Konoha. They look for a new house and start decorating a nursery. The whole village is happy for them.
The power system in Naruto is one factor. The idea of chakra and how it can be manipulated in various ways is quite experimental. It allows for a wide range of abilities and combat styles. Also, the character arcs often deviate from typical hero - villain dynamics. For example, some characters have complex motives that are not simply good or bad.
One plot could be that the time - travel aspect of the Lilo experiment is actually a part of a larger plan by an unknown entity. Lilo is sent through time to different points to gather specific information or items. As she travels, she realizes that her actions are being manipulated. She has to break free from this control and find a way to use the time - travel knowledge she has gained to save her world from an impending threat that was set in motion long ago.
It could involve an original character (OC) being subjected to genetic experiments by the asari. Maybe the OC has unique biological traits that the asari are interested in exploring, leading to a story of discovery, power struggles within the asari society regarding the experiment, and the OC's struggle for freedom or self - identity.
Love and redemption are very common themes. Since Sasuke has a rather dark past, many fanfictions focus on how he can be redeemed through Sakura's love. For example, in some stories, Sakura is the one who helps Sasuke come to terms with his past misdeeds and find a new purpose in life.