One interesting plot twist could be Naruto changing the past in a way that completely alters the future relationships. For example, if he manages to prevent certain tragedies from happening to his friends' families, it could lead to very different dynamics. Maybe Sasuke's family wouldn't be massacred, and Sasuke would grow up in a completely different environment, which might change his entire attitude towards the village and Naruto himself. This could lead to a whole new set of adventures and challenges for Naruto as he tries to adapt to this new timeline.
A possible plot twist is that Naruto's time travel affects his own powers. He could find that in the past, his chakra has different properties or that he has access to new jutsu that were lost in his time. This could make him a much more powerful and unpredictable force. On the other hand, it could also attract unwanted attention from those in the past who might see his new abilities as a threat. This would create a situation where Naruto has to balance using his new powers to fix things while also avoiding being hunted down by those who fear him.
Perhaps Naruto travels back and discovers that the origin of the ninja world's problems is something completely different than what he thought. He might find out that there was a more sinister force at work from the very beginning that was manipulating events. This could lead to him having to form new alliances and fight against enemies that he never knew existed in his original timeline. It could also change his perception of the older generation of ninja who might have been unknowingly influenced by this hidden force.