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 idea could be to create a crossover where Kagome somehow gets transported to the Naruto universe. Maybe she could use her spiritual powers from Inuyasha to interact with the chakra-based powers in Naruto. For example, she might help Naruto understand a different type of energy system, which could lead to new jutsu development for him.
Yes, it can be considered an experiment in some ways. One unique aspect is its character development. Naruto starts as an outcast in the village but grows into a powerful ninja. The story experiments with the idea of perseverance against all odds. Another aspect is the world - building, with different jutsus and ninja clans, which is quite innovative.
The theme of mystery is quite common. The reasons behind the animal experiments are often shrouded in mystery at the start. Is it for power? For some dark plot against the village? Naruto has to figure it out. Also, the theme of transformation is there. Some animals might transform due to the experiments, and Naruto has to deal with the consequences of these new, sometimes unpredictable forms in his efforts to protect the village and the animals.
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 idea could be an experiment on new jutsu creation. For example, Naruto and his friends could be part of a research project to combine different elemental jutsus in unique ways. Another could be an experiment on the limits of chakra control, like seeing how much chakra Naruto can store in a new type of seal.
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.
The story would also change in terms of Naruto's relationships. His friends like Sasuke and Sakura would be very concerned and might try to stop him. This could lead to a rift between them. Naruto might gain new powers faster, but at a cost. He could start to lose his connection to his normal self and the Nine - Tails inside him might react negatively to the experiment.
In some 'naruto bloodlines experiment fanfiction', there could be the concept of a failed bloodline experiment that leads to a character having unpredictable powers. This can add a lot of drama and mystery to the story as the character tries to control or understand these new abilities. Also, the fanfic might explore how different characters react to this new and potentially dangerous situation.
Some fanfictions in this genre might deal with the idea of using genetic experiments to revive extinct ninja clans. Imagine bringing back the Uzumaki clan in a new form through genetic manipulation. There could also be the idea of using genetic experiments to counteract the effects of certain curses or seals. For example, if a character has a seal that limits their power, genetic experiments could potentially find a way to break or modify that seal. Additionally, the idea of cross - species genetic experiments, like combining ninja genetics with that of some mythical beasts in the Naruto universe, could lead to really unique and exciting storylines.