Though I love the pairing, I stopped midway in the first chapter - Shinji is too much of a Mary Sue:
He is able to override his personality, as shown in the series (a teenager unsure of himself in a lot of ways), without any transition or explanation. (Other than a crude metaphor of "the Man" beating up "the Coward" in his mind - a metaphor that becomes tiring very quickly.)
Up to now, Misato, Hikari, Kaji and Asuka have said or thought "Oh my god Shinji is so nice/responsible/manly/admirable", with just enough emphasis that it becomes irritating.
Not so well-written
Though I love the pairing, I stopped midway in the first chapter - Shinji is too much of a Mary Sue: