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 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.
Financial difficulties could also be a problem. Naruto might not be well - off initially, and raising a child requires money for things like food, clothes, and education. He would have to find ways to provide for his sister while still being a ninja. Also, there could be threats from Naruto's enemies who might try to target his sister to get to him.
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.
Legal issues could be a major challenge. The adoption process can be complex, especially if there are issues with the girl's background or if Jason Wayne has any 'questionable' aspects in his own life according to the law. He may also face challenges within his own social circle. Some of his friends or colleagues might not be supportive of his decision, thinking it will interfere with his work or change his image. This could put a strain on his relationships as he tries to do what he believes is right for the little girl.
One of the main challenges is education. In a traditional classroom, she may not be able to fully understand the teacher without proper accommodations. Socialization can also be tough. She might feel left out in group conversations where everyone is speaking instead of using sign language. Another issue is access to information. A lot of media and information is presented in audio - only formats, which she can't access directly.
One challenge could be social acceptance. Some people in society might not be as accepting of a gay step - dad becoming a full - fledged 'daddy' in a family. Another is dealing with the child's own adjustment. The child may have mixed feelings about having a new person in such an important role. Also, legal issues might arise, especially regarding parental rights in some areas that may not be fully inclusive of gay relationships.
One challenge could be time management. Naruto is always so busy with his ninja duties, protecting the village and going on missions. Finding the time to sit down and write would be tough. Also, he might struggle with grammar and spelling since his ninja training didn't really focus on that.
One challenge could be gaining the trust of the Root members. Since Root has a history of being a secretive and somewhat feared organization, the members might be skeptical of Naruto's leadership. They're used to a more authoritarian style, and Naruto's more open and friendly approach could be met with resistance.
Mako might face vocabulary challenges. Fanfiction often contains unique words or terms specific to the fandom. Also, understanding different writing styles can be difficult as fanfiction varies greatly in style. Another challenge could be following complex plotlines that are sometimes created in fanfiction, especially those that deviate from the original source material.
One challenge is spelling errors. Dyslexia can make it difficult to spell words correctly, which might be a hindrance in writing fanfiction. Another is grammar. They may have trouble with proper sentence structure. Also, organizing their thoughts into a coherent story can be tough as dyslexia sometimes affects the ability to sequence information.