Link is by far the most popular. Since he is the main protagonist in the Zelda series, he is often the center of time travel stories. Writers like to explore his journey through different time periods, his growth as a hero, and how he copes with the changes that time travel brings.
Ganondorf can also be a prominent character. His villainous nature and powerful magic can create interesting plotlines in time travel fanfiction. For example, he might try to manipulate time to his advantage or be a constant threat that Link has to face across different time periods.
Jon Snow is very much a favorite in asoiaf time travel fanfiction. Given his complex backstory and his role in the fight against the Others, fans often write about him traveling back in time to change certain events. Arya Stark is also popular. Her skills as an assassin could be put to different uses in different time periods. For example, she could go back in time to protect her family members from harm.
The Lone Wanderer is quite popular. Their heroic deeds in the main Fallout games make them a prime candidate for time - traveling adventures. Also, Courier Six. Their mysterious background and skills could be explored in time - travel scenarios.
Jotaro Kujo is quite popular. His strong and stoic personality makes for interesting interactions in different time periods. Dio Brando is also a common choice. His villainous nature and powerful Stand, The World, can create a lot of chaos when time - travel is involved. And then there's Jonathan Joestar. His noble character can be a great contrast to the more modern and complex characters when he's brought into different timelines through time travel.
Link is obviously one of the most popular. He's the main hero in the original games, and in fanfiction, writers often put him in new and exciting situations. They might give him different personalities or explore his relationships with other characters in more depth, like his friendship with Zelda or his rivalry with Ganon.
Laval is a very popular character. He is the prince of the Lion Tribe and his bravery and leadership make him a great focal point for many fanfictions.
Spyro himself is of course a very popular character to feature. He is the main protagonist, and his journey of growth and discovery makes for great fanfiction material.
Jaina Proudmoore is often featured. She has a lot of emotional depth and her actions have had a great impact on the story. In time travel fanfiction, she might go back to when she was younger and make different choices regarding her relationships and her role in the war. Arthas Menethil is also a popular character. His fall from grace is a well - known and tragic story. Time travel could be used to explore if he could have been saved from his dark path, perhaps by going back to his early days and changing certain events or influences.
Boruto himself is obviously a very popular character to feature. Since it's a Boruto time travel fanfiction, he's usually the main focus. Naruto is also popular. When Boruto travels back in time, his interactions with his father Naruto at a younger age are often explored. Sasuke is another one. His skills and knowledge can be important in helping Boruto in the past, or Boruto might discover something new about Sasuke's past during his time travels.
Bran Stark is a popular choice too. Since he has the power of the Three - Eyed Raven, time travel can be related to his abilities. Fanfictions might have him traveling through time to gain more knowledge or to influence events in a more direct way. Jaime Lannister also features often. His character arc can be completely transformed through time travel, for example, going back to redo his actions as the Kingslayer or forward to see if he can redeem himself in a new Westeros.
George Washington is a very popular character. His leadership and moral character make him an interesting figure to put in a time - travel scenario. Benjamin Franklin is also popular. His scientific mind and worldly wisdom can create great storylines when he's thrust into a different time. Thomas Jefferson is another one, especially considering his complex views on various issues which can be explored in a new context when he time - travels.