Naruto himself is very likely to be central. Since he is the main character in the original series, any alteration of time would likely still revolve around him in some way. His journey and how it's affected by the time changes would be a major focus. Sasuke is also a prime candidate. His relationship with Naruto and his own quest for power and revenge could be greatly altered by time changes. Another one could be Kakashi. He has a lot of backstory and knowledge, and in an altered time, his role as a mentor or a ninja in general could be very different.
Definitely Naruto and Sasuke, as their fates are intertwined in the original story. In a time - altered scenario, their bond and their individual destinies would be ripe for exploration. Hinata could also be central. In the original, she had a strong, if somewhat understated, presence. In a time - altered fanfiction, her relationship with Naruto might be completely different, and she could play a more prominent role in the events of the ninja world. And then there's Itachi. His actions were so crucial in the original story that any time alteration could have a huge impact on his story and how it affects the other characters.
Well, Naruto is the obvious choice as he is the protagonist. But I think Jiraiya could also be central in time alter fanfiction. He has a vast knowledge of the ninja world and was a key figure in Naruto's development. In an altered time, his teachings and his own adventures could be very different. Also, Nagato. His role in the original story was significant, and in a time - altered world, his views on peace and his actions could be completely changed. He might not form the Akatsuki in the same way or might have different goals altogether, which would have a huge impact on the overall story.