I think the biggest problem that people have with NGE is that it just isn't your typical shounen anime. All of the characters behave in a way because of their past experiences. Shinji being abandoned by his father, witnessing his mother's death without actually understanding or realising it, asuka being neglected by her mother and Rei being a clone. And all of them in their teens, in a broken world getting told to fight and probably die or humanity is doomed.
With how saturated anime are with flawed main characters that then use that flaw to their advantage to overcome their enemy, NGE just doesn't do that.
I think that viewers just expect this hero story when they watch it.
I mean. I had a similar impression when I first watched it a long long time ago and thought that shinji was a wuss. But that was after I watched the typical shounen, DB, DBZ, Naruto and bleach. Not to mention that I didn't understand what the fuck was going on. Only later after watching it a second time and digging into the background a bit, shinjis Oedipus complex, asukas hedgehog dilemma and the general motivation of each of the characters it made a lot more sense. Including the context of their situation made me appreciate the storytelling a lot more because it put everything into perspective.