Okay, so episodes 25 and 26 of the TV series really happened, but what do they really mean? They e pretty farged up, ya know.
It’s a little difficult to explain, but in reality it’s not Shinji that’s questioning if others like him and why he exists at all if all he does is run away, it’s Hideaki Anno. Try this: Whenever Shinji says “I” or “me” in the final two episodes of Eva, substitute either “Studio Gainax” or “Anno”. Whenever the EVAs are mentioned, substitute “Project EVA” (the animation). And anytime Shinji wonders if “other people” like him, replace it with either “rival studios” or “the audience”.