Well, it depends on the specific fanfic. Some fanfics might focus on Naruto's growth post - Shippuden and give him abilities that make him stronger than Itachi. For example, they could have Naruto master a new form of Sage Mode that gives him an edge over Itachi's Sharingan - based techniques. However, other fanfics might keep Itachi's power level relatively high and not have Naruto overtake him. So, there's a lot of variation among different fanfics.
In a lot of fanfics, Naruto is stronger than Sasuke. Naruto has always had an incredible willpower and in fanfics, this can be translated into him achieving greater power levels. His ability to make friends and allies can also lead to him getting more support and resources in the story. For example, he might get some special training from an ancient sage that Sasuke doesn't have access to. Also, his positive attitude can attract more powerful beings to help him out, which gives him an edge over Sasuke in terms of strength.
Often, in fanfic, Naruto is made stronger than Itachi because the writers want to explore new story arcs. If Naruto is stronger, new and exciting battles and relationships can be created. For instance, Naruto could be the one to protect Sasuke from Itachi in a different way. Also, Naruto's positive and determined nature makes him a popular character to be super - powered in fanfics.
One reason is that Naruto has the Nine - Tails' chakra. In fanfic, this power can be further enhanced or manipulated in ways that make him far more powerful than Sasuke. Another reason could be his more outgoing personality. He might be able to form alliances more easily, leading to him having more resources and power - ups at his disposal.
Naruto is stronger in fanfiction because of his ability to connect with others. He has made friends all over the ninja world. This network of friends often provides him with support in battles, whether it's intel or actual combat help. Also, his training under Jiraiya was very comprehensive. Jiraiya taught him not only combat skills but also how to be a better person. This made Naruto grow both physically and mentally. And compared to Sasuke, Naruto seems to be more adaptable to different fighting styles in fanfiction, which gives him an edge in combat.
The relationship might become more equal. Since Sakura is stronger, Sasuke can't look down on her as he might have in the original story. They could become more like true partners, respecting each other's abilities.
Another plotline might be Naruto's strength leading to a different kind of peace in the ninja world. Since he's stronger, he can enforce his ideals more effectively. He could start a new era of cooperation among the ninja villages by using his power to make the other villages see the benefits of unity, and Sasuke might be reluctantly following his lead.
There are fanfictions where Naruto, using his Uzumaki clan's sealing techniques along with his chakra, is able to break through Sasuke's genjutsu. Genjutsu is one of Sasuke's strong points usually, but Naruto's unique abilities give him the upper hand. Also, in certain stories, Naruto's connection to the nature energy in his Sage Mode is so strong that he can heal himself during a fight with Sasuke, while Sasuke doesn't have such a convenient self - healing ability.
In this fanfiction, Itachi might help Sakura become stronger by training her in various ninja skills. He could teach her advanced genjutsu techniques. For example, he might start with the basics of detecting and breaking genjutsu, and then gradually move on to creating complex illusions herself. This would enhance Sakura's ability to defend against and use genjutsu in battles.
In this kind of fanfiction, Itachi might use his powerful Sharingan abilities. He could perhaps create illusions to mislead Orochimaru and his minions, then quickly snatch Sasuke away. For example, he could make Orochimaru think that Sasuke is in a completely different location while he secretly approaches and rescues him.