Sasuke could be a likely character in some fanfiction. Maybe in an alternate universe where their rivalry takes a darker turn, Sasuke might frame Naruto to gain an advantage or to prove his own superiority. It would add a whole new dimension to their relationship.
Danzo is another possibility. He was always a bit of a shady character in the original series. In fanfiction, he could frame Naruto to get rid of him as he sees Naruto as a threat to his power and influence within the village. He might spread false rumors about Naruto being a danger to the village's stability.
Obviously Naruto himself is the main character involved. But his friends like Sasuke, Sakura, and Kakashi are also likely to be involved. Sasuke might be affected by Naruto's wishes, for example, if Naruto wishes for Sasuke to fully return to the Hidden Leaf Village and be at peace. Sakura could also be involved, perhaps in helping Naruto make his wishes come true in a medical or support way. And Kakashi, as Naruto's former teacher, would surely play a role in guiding Naruto in how to use his wishes wisely.
Definitely Naruto is the central figure. In the harem, Hinata is a very likely character since she has always been in love with Naruto. Sakura might also be there as she has been one of Naruto's closest friends. Tenten could be another addition. She has interacted with Naruto in the series and could potentially be part of the harem in this fanfiction. Also, Temari, who has had some interesting encounters with Naruto, might be a character in the harem as well.
Iruka could be a surprising character to abandon Naruto in some fanfictions. Maybe he gets influenced by some outside force or a misunderstanding that makes him think Naruto is no longer the Naruto he knew. And then there are the other genin in Naruto's class. They might abandon him out of jealousy if Naruto starts showing extraordinary powers too quickly. Or they could be pressured by their families who don't want them associated with Naruto.
Sasuke would definitely be one of the main characters to interact with Naruto. Their relationship has always been complex, and with Naruto as a girl, it could become even more so. Sakura would also interact a lot. She might be both jealous and intrigued by Naruto's new form. Kakashi too, as Naruto's mentor, would have to adjust to this change and guide 'her' in a different way perhaps.
It could be a jealous rival from another guild. They might see Natsu as a threat and figure framing him would be a good way to get him out of the way.
One of the likely supporting characters is Tsunade. Given her experience and leadership in the village, she could be a source of advice for Naruto and Hinata. She might also ensure that Hinata has the best medical resources available during her pregnancy. Rock Lee could be another supporting character. His positive attitude and loyalty to Naruto would make him eager to help out. He could be running errands for them or helping with any physical tasks. And Neji, if he were still alive in this fanfiction, would surely be there to protect his cousin Hinata and support Naruto as well.
Kakashi could also be an important character. He has a lot of experience and wisdom. When Naruto gets high, Kakashi might be the one to guide Naruto through this strange state, using his own past experiences and knowledge of different ninja techniques. And then there's Jiraiya. Given his relationship with Naruto, he would surely be involved, perhaps trying to use his own unique jutsu to help Naruto come back to normal.
Hinata would also play a major role. Since she has deep feelings for Naruto, she would be devastated by his amnesia. She might try to use their shared memories, like the time she confessed her love to him during the Pain attack, to jog his memory. And the Akatsuki members could also be involved in some cases. If Naruto's amnesia was caused by their actions, they might be the antagonists in the fanfiction, or they could also be trying to use his amnesia for their own purposes.
It could be Orochimaru. He's always been a sneaky and devious character. He might frame Naruto to create a distraction while he tries to steal some valuable secrets from Konoha. Another likely villain could be Danzo. He has his own motives and is not above using underhanded tactics. He could frame Naruto to get rid of him as he sees Naruto as a potential threat to his power and control over the village.
Sasuke is very likely to be involved. Given their complex relationship, Sasuke could be the one who finds Naruto severely injured and has to make a choice between helping him or leaving him. Another character could be Sakura. As a medic - ninja, she would be the one to try and heal Naruto's severe injuries. Kakashi too might be involved, either as a mentor figure who tries to figure out what happened to Naruto or as someone who has to step in to protect Naruto from further harm while he is injured.