Shinji is (or will become once he is older) a homosexual (or at least mostly homosexual). Other than the bath scene between Kaworu and Shinji, compare Shinji's interactions between the two. With Asuka, Shinji is always uptight and hesitant due to the fear of Asuka; even if this is viewed from Shinji wanting a strong women to counter his weak personality, Shinji never feels comfortable around her. Shinji feels little empathy towards and from Asuka in both stagnant life and specific situations. At home, Shinji is very kept to himself and away from the feelings of Asuka (and Misato for the most part); Shinji has little will to talk with Asuka and help with her problems or have Asuka help with his. In specific situations, Shinji does not act the same as a "regular" boy would; For example, the kiss between the two was done rather forcefully from Asuka and had no lasting effect on Shinji (at least in the same way a first kiss should). Of course, he is growing up and has sexual hormones like everyone does (as seen with Shinji masturbating to Asuka comatose body), but like with all people, Shinji's sexual urges are not refined yet.