Shinji Ikari is one of the most hated anime characters of all time (in the west at least; I don't know about his country of origin), but he's been one of my favourite characters for a long while. I like him 'cause his portrayal doesn't shy away from what a scared, broken kid might do in this situation, and it creates a visceral emotional realism that's so far been unmatched. This is not to say I only like him for clinical reasons, though; I do have a genuine fondness for Shinji, considering him more than just an object to study. However, that doesn't mean Shinji is free of any moral issues, far from it.
I used to feel far more guilty about being a Shinji fan than I do now. I lost a lot of this guilt when I realized how dumb it was to fret over being a fan of a character. Sure, the fact that Shinji didn't always do what was right might have been deplorable in a real person, but he was just a character. And, now that I'm twice as old as he is, I have a lot more detachment from this actions, usually just looking at him and think "Sheesh, poor kid," instead of faking a hard-line moral stance. But even so, there are some things regarding Shinji that makes me question liking him, and they are questions I can't answer.
His behaviour in End of Evangelion is reprehensible. There is the worst: he masturbates over an unconscious person. It makes total sense given the point the character is at, and is effective, but it's also…just…augh. When reminded of the scene, I ask myself how I could rank him so highly with this happening.
What I will say is that the scene makes sense. At that point in the series, Shinji has hit rock bottom, but is still attracted to Asuka. The way I interpret it, he's bought into her hype about being heroic and strong, whom he desires even though she's hateful towards him—in fact perhaps because she's hateful towards him, since Shinji seems like the masochistic type.
In Shinji's self-destructive, self-hating state, the sexual impulse becomes twisted, and he gives it release in one of the worst ways he can. It is a disgusting scene, but it makes sense. That doesn't excuse it, but it didn't come out of the blue. I can understand why some fans rejected Shinji after the movie, but it wasn't out of character for him to do that.
In the same film, Shinji is so destroyed that he does nothing in the first half but let himself be dragged around like a sack of potatoes. While this reaction also makes sense, and I'll defend it on those grounds, it's also true that Shinji opened Asuka up to death, compounding the way he harms her. Some of the deaths at NERV in the raid should be on his head, too, for if Shinji had entered battle earlier, he might have saved more people. Yet even though Shinji has done worse on a larger scale, and I still hold that against him, the smaller, more personal crime is what makes stands out. That's not surprising; it might just be human nature, so that it's easier to get a strong reaction to a more intimate harm.
Knowledge of the scene just sits there, like a big immovable stone right in the middle of my headspace. I can't ignore, it, I can't move it, I can't wish it away. It doesn't destroy my interest in Shinji, but it's not forgotten. It's just…there. I don't try to excuse it, but it can't change anything.