Sure. A lot of fan - created stories might center around their emotional bond. Maybe it shows how Shinji looks up to Misato for guidance and support during his difficult times in NERV. These stories can be really interesting as they delve into the characters' personalities and the unique dynamic between them without having to be lemon - related.
Their shared experiences in the fight against the Angels also add depth. They've both been through so much trauma and danger together. Fanfiction can explore how these experiences might bring them closer or create new conflicts between them. For example, Shinji might feel indebted to Misato, while Misato could be overprotective of Shinji due to what they've faced.
A different plot could involve a time - travel or alternate - reality scenario. Maybe Shinji and Misato are sent to an alternate timeline where their relationship is very different from what it is in the original Evangelion Rebuild. They have to figure out how to get back to their own timeline while also dealing with their changing feelings for each other.
Well, one positive aspect is that they can represent a kind of family bond in some fanfics. Since Shinji lacks a proper family, Misato can fill that role to some extent. She provides a home for him and shows care. Also, their relationship can be a source of character growth for both. Shinji learns about responsibility and Misato might learn more about herself as she tries to help Shinji. This mutual growth is really interesting in the fanfics.
In general, the Evangelion mangas are considered good. They expand on the anime's universe, providing more depth and character development. However, it depends on personal preferences as some might find the style or pacing not to their liking.