Well, Jiraiya is often a popular character in these types of fanfictions. He is Naruto's mentor and has a lot of knowledge about the ninja world. In a time - travel story, he could learn from Naruto about the future and use that to his advantage, or he could teach Naruto things he didn't learn before. Also, Sakura could be a popular character. She might follow Naruto and Sasuke back in time and have her own role to play, like using her medical skills to save people who died in the past.
I think Kakashi could be really popular. Since he has a connection to both Sasuke and Naruto, his role in a time - travel story could be very interesting. He might be able to help them adjust to the past or use their knowledge to his advantage. Another popular character could be Itachi. His actions in the past are so crucial to the story, and in a time - travel scenario, he could interact with Sasuke in a whole new way.
Definitely Tsunade. She's a powerful character and her knowledge of the village's history and politics could be a great asset in a time - travel story. She could also be a bit of a challenge for Naruto and Sasuke as she might not believe their claims of coming from the future right away. And Orochimaru is another character that might be popular. His thirst for knowledge and his experiments could be intertwined with the time - travel plot in some very interesting ways.