A powerful warlord who wants to conquer both Ceez's world and the ninja world. He has an army of dark warriors and uses dark magic to try and achieve his goals. He sees Ceez and Ninja as the biggest threats to his plans, so he constantly tries to eliminate them.
An ex - ninja who was banished from the clan for using forbidden techniques. This ex - ninja, filled with revenge, teams up with a group of outlaws. He has a personal vendetta against Ninja and when Ceez enters the picture, he sees it as an opportunity to cause more chaos. He uses his knowledge of the ninja arts against them, making him a formidable villain.
One idea could be that Ceez is a new recruit in a ninja clan led by Ninja. Ceez has some unique powers that the clan has never seen before, like the ability to communicate with animals. This causes some jealousy among the other ninjas at first but eventually helps the clan in a big battle against an evil sorcerer.
It could be Shredder as always. He might see the sister as a new threat or a way to get to the turtles. He could try to kidnap her to lure the turtles into a trap.
Krang from Dimension X could also be a great villain. He might be interested in the human sister because she has some unique knowledge or ability that he wants to use for his own evil plans in taking over Earth. He could send his minions to capture her and the Turtles would have to journey to Dimension X to save her.
Without more details about 'ceez light novel', it's impossible to determine the main characters. They could be a young hero, a wise old mentor, or a group of misfits on an adventure, but that's just pure guessing at this point.
It could also be a powerful and jealous ninja from another village. This ninja is envious of Naruto's growing power and popularity. He decides to create a false narrative about Naruto being a threat to all the villages and starts a war against him. Naruto would then have to prove his innocence and stop the war before it destroys the ninja world.
Maybe an entire rival village decides to target the prodigy. They see the potential threat that the prodigy poses to their own village's dominance, so they send their best ninjas to take the prodigy down.
It could be a new character, an ice ninja named Hakuji. He has a tragic past, his family was killed by a rogue ninja group and he was left alone in the cold northern lands. He comes to Konoha seeking revenge at first but then befriends Naruto and changes his path.
Shizune. She was Tsunade's assistant and a very capable medical ninja. A fanfic could focus on her backstory, like how she became a medical ninja and her experiences during the various battles she was a part of. She could also have her own adventures away from Tsunade.
Hermione Granger could also be a main character. With her intelligence, she would be quick to learn ninja techniques and could even help improve them with her knowledge of magic. She might study the ancient ninja scrolls and find ways to combine the knowledge of both worlds for the greater good.
A young and determined trainer named Kai could be a main character. He has a Pikachu that he has trained to use ninja - like moves, such as lightning - fast dodges. Kai is always eager to take on new challenges and prove himself as a great pokemon ninja trainer.