I think that’s part of it? Like I haven’t seen it but Shinji’s choices are objectively wrong but also make sense because he’s a flawed human. So you’re supposed to disagree with him but also sympathize but also disagree with him.
I definitely agree. I can understand why people relate with him now that I think about other morally gray characters I can empathize with. For example, Joel from the TLOU. He basically doomed mankind, but if I was in his situation I would’ve done the same exact thing, even if I had the knowledge of what the consequences would be.