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.
One popular 'Evangelion Female Shinji Fanfiction' is 'Shinji Ikari: Girl Savior'. It presents an interesting take on Shinji being female, with different character dynamics within the Eva universe. Another one could be 'Female Shinji's Adventure in NERV'. It explores how a female Shinji might interact with the other characters like Asuka and Rei in a new way.
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.
He could meet his future self. His future self might be wiser, having learned from all the experiences in the past. They could have a deep conversation about Shinji's purpose and the mistakes he's made.
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.