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.
One of the main themes could be the concept of the magical girl system itself. It might explore how the system is structured and what it means for the girls involved.
Often in such stories, there are supporting characters like the friends or family members of the magical girls. They may not have magical powers but can influence the magical girls' decisions and emotional states. For example, a best friend from school might notice the strange behavior of the magical girl and try to figure out what's going on, adding an extra layer of complexity to the story.
One main theme is often identity. Since Shinji is female in these fanfictions, there's exploration of how she sees herself in a world that was originally designed around a male Shinji. Another theme is relationships. Her interactions with characters like Misato or Gendo could be different.
He could also become more social. In the Highschool DxD world, there are many different species and characters to interact with. Shinji, who is often isolated in Evangelion, might start to open up and form friendships or alliances. This would be a big change from his usually withdrawn personality.
Well, in some fanfictions, the kiss might be a symbol of redemption. Shinji has his own insecurities and Asuka her pride. When they kiss, it could be like they are redeeming each other from their own self - loathing. It might also be a way to show that despite all the chaos and the end - of - the - world scenarios in Evangelion, love (or at least a form of it) can still find a way. For example, it could be the start of a new phase in their relationship where they support each other more and face the challenges together.
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.