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.

It's generally clear that he does not like the fanbase either.
Quote Originally Posted by Anno
Anime fans and the anime industry are also indefinite. In a manner of speaking all of Japan is indefinite. I hated this, and I wanted to construct a barrier between myself and society. Expressing it in terms of the show, it was an “AT Field,” a pattern [of behavior] where I would tear apart or reject anything that crossed the boundary line between myself and others. Perhaps [that was the] “barrier of the heart.”