Well, strange as it may sound, the NGE manga is
not the "official" or "real" story in the same sense that the TRC manga is the real thing as opposite to Bee-train's anime.
In the case of NGE, the anime came first, followed by the manga (an interesting note, however, is that the author of the manga was also involved in the making of the anime - he did the character design). Unusual, huh?
In any case, I think the anime made it perfectly clear even without kissing that Shinji was interested in Kaworu in a more-than-platonical-way, but, as much as I liked both characters, I never really cared for them as a couple, as I keep thinking of Kaworu as, not a person, but a symbol. Exactly what it is he symbolises I don't know, though. It could be self-acceptance, it could be love... or it could just be coolness.
