It depends on your perspective. Sometimes Ikari's actions might seem villainous, but there could be underlying reasons or circumstances that explain his behavior and make him more of a morally ambiguous character.
One possible reason could be the long - standing emotional neglect Shinji has endured from Gendo. In the Evangelion series, Gendo is often distant and cold towards Shinji, and in fanfiction, this could build up to a point where Shinji snaps.
A 'naruto doujin ikari fanfic' could be about many things. It might focus on Naruto's anger (ikari in Japanese) in a non - canonical story created by fans. Maybe it's about a situation where Naruto is pushed to his limits and his anger drives him to take on new challenges or face his enemies in a different way.
A 'naruto soujin ikari fanfic' could be a really interesting piece of fan - created literature. Since Naruto is a rich universe with so many characters and storylines. 'Soujin' might imply something related to the essence or nature of a character. And 'ikari' being involved, it might center around a conflict that is driven by anger. For example, it could be about a character who discovers something about their past that makes them angry and sets them on a path of revenge or self - discovery within the Naruto world. It could also be a story that delves into the psychological aspects of anger and how it affects a character's relationships and decisions in the Naruto - inspired setting.
There are fanfictions where Shinji Ikari has different relationships with the other characters. In some, he forms a closer bond with Asuka earlier on and they work together more effectively against the Angels. This changes the whole dynamic of the story as their combined strength and new - found friendship alters the course of events.
One idea could be that Shinji Ikari is transferred to the Highschool DxD school as an exchange student. He might initially struggle with the very different supernatural environment compared to his Evangelion world. His experiences with Angels could give him a unique perspective on the devils and other beings in the Highschool DxD world, leading to some interesting interactions and storylines.
It can create a major turning point. If Shinji has always been submissive before, his snapping can change the power dynamic between him and Gendo. This might lead to Shinji taking more control of his own actions and decisions in the story.
One idea could be a crossover with a superhero universe. Shinji Ikari could gain superpowers and have to navigate the complex world of superheroes, dealing with their moral codes. Another could be a crossover with a fantasy world like Middle - earth. He might find himself on a quest with hobbits or elves. A third idea is a crossover with a post - apocalyptic world, where Shinji's experiences in his own apocalyptic - like setting of Neon Genesis Evangelion could be put to use in a different kind of desolate landscape.
You can try looking on fanfiction websites. Some popular ones like FanFiction.net or Archive of Our Own (AO3) might have 'naruto doujin ikari fanfic'. Just search for the relevant keywords in their search bars.