I think Naruto would be more independent in his thinking. Kisame doesn't seem like the type to spoon - feed answers or rely on a group in the same way Konoha does. So Naruto might develop his own unique moral code that is a blend of Konoha's values and what he learns from Kisame. He would be more likely to question authority and make decisions based on his own judgment rather than blindly following the rules of the village.
His personality would likely be more stoic. Kisame is a rather reserved and tough character, and growing up with him would probably make Naruto less exuberant. He might not be as quick to trust others as he is in the original story.
Naruto could be more secretive. Since Kisame is from a group that operates in the shadows (the Akatsuki), Naruto would be taught to keep things close to the vest. He may not be as open about his feelings and plans, which would be a big shift from his normally open - book personality in the main Naruto series. He would also be more attuned to the darker side of the ninja world and might have a more cynical view of things.
His sense of humor would be different. Anko has a dry and sometimes dark sense of humor. So Naruto might crack jokes that are a bit more on the sarcastic side and less goofy. For instance, instead of his usual over - the - top pranks, he might play more calculated and sneaky pranks inspired by Anko. Also, he would be more confident in his own abilities from an earlier age, as Anko would encourage him to trust his instincts.
He'd probably be more confident. Kushina's love and support would make him feel secure. He wouldn't have that same loneliness - driven need for attention like in the original story.
Naruto would likely be more confident. Growing up with his parents, he wouldn't face the same neglect and ostracism. So he wouldn't have to constantly seek attention in a loud or brash way.
He could be more secretive. Lex Luthor often has his own hidden agendas. Growing up with him, Naruto might learn to keep his plans and thoughts to himself more. This would be a departure from the open - book Naruto we know, who usually wears his heart on his sleeve. However, he would still have his core of kindness, but it might be expressed in more subtle ways. For instance, instead of loudly proclaiming his desire to protect everyone, he might quietly work behind the scenes to achieve the same goal.
Naruto's training would likely be more intense and survival - based. Zabuza was a tough and unforgiving trainer in his own right. He might push Naruto to his physical and mental limits from a young age, making Naruto more resilient in combat. For instance, instead of the relatively structured training in the Hidden Leaf, Naruto could be thrown into real - life combat situations early on to learn quickly.
He'd probably be more aggressive. The xenomorphs are aggressive creatures, so Naruto might not be as friendly as in the original story.
He'd be more disciplined. Samurai culture emphasizes self - control, so Naruto would be less impulsive.
His personality might become more refined. Instead of being the rowdy Naruto we know, he could be more composed and polite due to the influence of the daimyo's court.
Naruto could be more empathetic towards the Uchiha's cause. Since Mikoto is his mother figure, he would be exposed to the Uchiha's history and their grievances from a young age. This would make him more understanding of Sasuke's later actions and more likely to try and find a peaceful solution for the Uchiha's problems.
He might be more aloof. Since a phoenix is a rather otherworldly creature, Naruto could pick up some of its more detached qualities. He may not be as quick to make friends as in the original story, instead observing more from a distance before approaching others.