Naw I think they are. This is Anno after all, and he explicitly stated, "I tried to include everything of myself in Neon Genesis Evangelion—myself, a broken man who could do nothing for four years."
source of translation. In essence, he put much of himself into the story, mainly the parts of himself that he loathed. It's not saying that they can't be characters you can related to, because it's clearly how Anno sees it. However, through his words, it's clear his intentions were to make them unlikeable characters.
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