One reason is the exploration of 'what if' scenarios. In these fanfictions, Naruto and Shikamaru can go back and change the course of history. For example, they could prevent a character's death or stop a major battle from happening. It also gives a chance to see how their relationship might have developed differently in the past. And the time travel element adds an extra layer of mystery and adventure, as they have to figure out how to navigate the past and get back to their own time.
Madara Uchiha could be an antagonist as well. Even if they travel back to a time before his grand plans were fully in motion, he would still be a very powerful and dangerous foe. He might sense that Naruto and Shikamaru are from the future and try to use their knowledge for his own purposes, or simply eliminate them if they stand in his way.
One great 'Naruto Shikamaru Time Travel Fanfiction' is 'Shikamaru's Time - Traveling Adventure'. In this fic, Shikamaru goes back in time and uses his intelligence to change the course of many events in the Naruto world. It's really interesting to see how his knowledge of the future affects his decisions in the past.
One great Shikamaru x Naruto time travel fanfiction is 'Back to the Beginning'. In this fic, Naruto and Shikamaru are sent back in time due to a jutsu gone wrong. It's really interesting to see how they use their future knowledge to change things. Another one is 'Time - Twisted Bonds' where they go back and have to deal with past enemies in new ways, with a great focus on their friendship development.
One idea could be that Naruto and Shikamaru travel back to the time when the Uchiha clan was still intact. They could try to prevent the massacre. Maybe Naruto uses his future knowledge of Sasuke's pain to convince the clan leaders to find a different solution.
One great Naruto Shikamaru yaoi time travel fanfiction is 'A Different Path'. It takes Shikamaru on an unexpected time - traveling journey where he meets a different version of Naruto and their relationship evolves in a really interesting yaoi - themed way.
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.
Well, it could be Orochimaru. Even if they travel in time, Orochimaru's thirst for power and knowledge might make him an antagonist. He could see Sasuke and Shikamaru as threats to his plans, especially if they are trying to change the past which might interfere with his own schemes.
There's also 'Time - Twisted Shikamaru'. This fanfiction has Shikamaru accidentally sent into a time loop. Each time he loops, he tries different strategies to break free and also to save some of the tragedies that occurred in the Naruto storyline. It's a really engaging read as you see him struggle with his knowledge of the future and how to use it without causing more chaos.
The concept of time travel itself is very appealing. In the case of Shikamaru, it adds a new layer to his character. We already know he's intelligent, but seeing how he uses that intelligence in a time - travel scenario, like predicting events based on his knowledge of the future, is really cool.