Itachi and Kisame could be a pair with a close bond. Itachi is a very reserved person, but Kisame seems to respect and understand him to some extent. They often work together on missions, and this could be seen as a form of 'family' bond within the Akatsuki. Another possibility is Deidara and Sasori. Despite their differences in art forms, they seem to have a connection. Deidara looks up to Sasori in some ways, like a younger brother might look up to an older one.
In the Akatsuki, Itachi and Obito could potentially have a deep family - like bond. Itachi was doing Obito's bidding for a long time in order to protect Konoha from the shadows. There was a level of trust between them, even if their goals were not completely the same. And although Obito was using Itachi to an extent, there was still a connection. Also, Hidan and Kakuzu, for all their bickering, have a sort of 'family' bond. They are partners on missions, and over time, they've come to understand each other's quirks, which is like a family relationship in a way.
Definitely Hinata. If she's part of Naruto's family in the fanfiction, she would be extremely overprotective. She loves Naruto deeply and would do anything to keep him safe. Also, Jiraiya. He has a special bond with Naruto and might be overprotective. He knows Naruto's importance and would not want anything bad to happen to him. He would try to shelter Naruto from threats both physical and emotional.
Sakura and Sasuke are very likely allies. Sakura has her medical skills and combat abilities, and Sasuke, despite his past issues, has great power. They've been comrades with Naruto for a long time.
Obviously Naruto himself. Then his parents, Minato and Kushina. His wife Hinata and their children would also be part of it. Jiraiya could also be involved as he was like a father figure to Naruto. And maybe some of the remaining Uzumaki clan members if they are still alive in the fanfiction. Also, characters like Iruka, who was an important person in Naruto's early life, could be there to witness the family reunion.
Another pair could be Naruto and Kisame. Kisame is a very loyal member of the Akatsuki. If Naruto were to interact with him, he might be able to break through Kisame's loyalty to the Akatsuki's more extreme ideals and show him a different path. Their connection could be based on Naruto's unwavering belief in friendship and Kisame's longing for something more meaningful in his life.
Pein could be another one. As the leader of the Akatsuki, he might see baby Naruto as a means to an end. He could either want to use Naruto for his own grand plans or, in a more interesting twist, be swayed by Naruto's innocence and change his perspective on the Akatsuki's goals.
Definitely Itachi. He has a complex character and his own sense of justice. He might see Naruto as a key to changing the shinobi world in a different way than what the Akatsuki originally planned. Another one could be Kisame. He is loyal to Itachi and would likely follow Itachi's lead in taking care of Naruto.
Itachi could be a likely candidate. He has always had a complex relationship with Naruto. He knows Naruto's potential and his importance in Sasuke's life. Itachi might see Naruto as a key to changing the Akatsuki from within. He could approach Naruto with his calm and mysterious demeanor, explaining to him the real goals of the Akatsuki that are hidden beneath their violent exterior.
Pain would still be a likely candidate. His Rinnegan gives him a powerful and commanding presence. He has the ability to see the big picture and make strategic decisions for the group.
Sakura and Deidara. Deidara is an artist with a very unique view of the world. Sakura might be intrigued by his art while at the same time being repelled by his violent and destructive tendencies. Their conversations could be a mix of philosophical debates about art and power, and physical confrontations as they are on opposite sides.
Naruto himself could be a victim of family betrayal. His father Minato or mother Kushina might be involved in some alternate - universe plot where they turn against him for some dark reason. Sasuke's family is also a likely candidate. Itachi's actions could be re - imagined in a way where his real motives are more about betrayal of the Uchiha family rather than protecting it. And Hinata's family might be involved too, like if Neji, before his death, was made to betray the Hyuga family in some fan - created scenario.