Mr. Tines: Clearly, piloting this thing is not fun for at least this particular pilot. And cue the foreshadowing
Reichu: That's my cue to insert the obligatory reference to Thumbnail Theater:
Shinji: No, I have to fight. This is an amazing coincidence that will allow the person who hates me to understand my pain.
Toji: Wow, thanks to this amazing coincidence, I understand Ikari's pain.
Shinji: Strangely, I still hate my life.
Incisivis: On Reichu's comment for 289, I thought the same thing. For a while I was confused by this scene, wondering what was Shinji's reason to cry. I eventually decided it was because he fears his own capacity for violence. Intellectually he knows it's an "Angel" he's defeated and not a "human" (because at this point in the series, most characters think there's a difference), but the connotations of the violence and rage remain with Shinji and overwhelm his "rational" understanding. It's quite a contrast to episode #19 and EoE.
OMF: I think you're overanalysing this. Fear of violence and of his capacity for it might be part of it, but basically Shinji is a scared kid who's just been through hell. Maybe it's a cultural thing, but a lot of people seem to be puzzled by the fact that he's crying here! It's obvious why: He's a human being, and quite a gentle and caring one at that. It's a pity that, for some reason, so many see his qualities as negative. Shinji really isn't cut out for all this. He should be arranging flowers in breakfast nooks, not risking life and limb in brutal combat.