Naruto might face the challenge of finding suitable teachers in fanfiction. Genjutsu is a complex art, and not many in the ninja world might be willing to teach him, either because they underestimate him or because they are afraid of his growing power. Another challenge could be adapting to the different styles of genjutsu. There are many types of genjutsu, and Naruto would have to study and practice each one to become a master. He would also need to learn how to break free from powerful genjutsu himself, as this knowledge is crucial for a genjutsu master.
One challenge could be overcoming his natural inclination towards ninjutsu and taijutsu. Since he's always been more focused on those areas, switching his attention to genjutsu might be difficult.
In fanfiction, Naruto may face the challenge of dealing with the mental strain of genjutsu. Genjutsu requires a high level of mental focus and control. Given Naruto's sometimes impulsive nature, he would need to learn to calm his mind and think clearly. Also, he might face opposition from those who don't believe he can master genjutsu due to his past lack of proficiency in it.
The social ostracism would be a big challenge. Little sisters are seen as both valuable and somewhat abominable in Rapture. Other characters might shun or try to take advantage of the newly - made little sister. And she would have to constantly be on guard against splicers who want to steal her ADAM.
One challenge could be acceptance from other trainers. Since it's not the norm for a Pokemon to become a trainer, some might be skeptical or even hostile. Another challenge is understanding human strategies and rules of training. Pokemon are used to being trained, not doing the training themselves. Also, there could be communication barriers at first, even if they can communicate to some extent, understanding all the nuances of human language and commands for training other Pokemon might be difficult.
One challenge could be controlling the amount of natural energy he uses. If he uses too much, he might lose control and enter a berserk state like when he first tried to use Sage Mode. Another challenge is that his opponents might find ways to disrupt his connection to natural energy sources, leaving him weakened.
One challenge could be adapting to the team's dynamics. Team 8 has its own way of operating, and Naruto is used to his own style with his friends. For instance, they might be more methodical in their planning, while Naruto is more of a 'jump - in - and - figure - it - out' type. So, he'd have to learn to follow their lead sometimes.
One challenge could be Naruto's stubbornness. Naruto has his own ideas and ways of doing things, and getting him to listen and follow Kakashi's guidance might be tough. Another is dealing with Naruto's past traumas. Kakashi would need to help Naruto overcome his feelings of loneliness and being an outcast. Also, Kakashi has his own responsibilities and missions, so finding time to be a proper adoptive father could be a struggle.
One challenge could be cultural differences. Naruto is from Konoha and Temari is from Suna. Their different upbringings and village cultures might influence how they raise a child. For example, Naruto might be more lenient based on Konoha's more laid - back culture, while Temari could be stricter as Suna has a harsher environment. Another challenge is their ninja lifestyles. They are often away on missions, so they need to find reliable people to look after the child when they are gone.
In harem fanfiction, Naruto could face the challenge of dealing with different cultural backgrounds of his partners. Since they come from various places, integrating their ideas and values into the new clan structure might be a headache. Moreover, resources are always an issue. Rebuilding a clan requires a lot of money, manpower, and materials. He has to figure out how to gather these resources while also maintaining his relationships in the harem. For example, some of his partners may have their own financial or family obligations that could either help or hinder his clan - rebuilding efforts.
He might face challenges like finding the right place to plant the tree. Konoha has a lot of regulations about what can be planted where. Also, he needs to make sure the tree gets enough water and sunlight. If it's a magical tree, he may not know exactly what it needs to grow well.
One challenge could be controlling the power of the Juubi. It's an incredibly powerful and chaotic force. Naruto would have to struggle to keep it in check so that it doesn't overwhelm him and cause him to lose control. If he loses control, he could end up harming his friends and allies instead of protecting them.
One challenge could be dealing with competitors. If his company is in a competitive field like ninja training, there might be other established companies or individuals who see him as a threat and try to undermine his business.