When I watched NGE, I had no problems with Shinji. I don't get where this concept that he alone is some kind of symbol for all that's wrong and whiny and emo. Asuka, on the other hand, I hated. But then, I don't like fucking tsundere types.
Maybe the people who really don't like Shinji have watched some other giant robot anime and expected him to be "GAR" like several of the so called protagonists. But NGE can't be compared to other such shows, because this was made by a Japanese man with mental issues who turned them into a series about fighting religious mythology. Shinji wasn't meant to be the tough macho type, he was more a personification of insecurity, and overcoming it.