I watched it a while ago, and I didn't like it. My reasons go far beyond "Shinji is annoying" (he IS annoying, don't get me wrong), but the whole thing just comes across as kind of wrong in my eyes.
It uses a lot of religious imagery, but it feels like it's there purely for aesthetic reasons, without saying anything at all. It's just giving various things religious names for no reason at all, other than looking and sounding complicated and nice.
As for Evangelion's philosophy; it really pushes it, especially in EoE, but it never goes beyond surface level, and never feels like it adds to the story; it's just kind of there. "Reality exists in the human mind, and nowhere else" is basically paraphrased with some rearranged words, but it feels pointless. In 1984, said quote was used to illustrate a clear point regarding book's central themes. In Evangelion, it's just there to sound smart.
As for Shinji; his whining wouldn't be so bad if not for the fact that he never does anything; he's unable to think for himself, he never aspires to anything. He starts off depressed, remains in said state throughout the entire story, and doesn't even try to do anything about it (which kind of defeats the point of the whole "deconstruction" thing.)
He doesn't HAVE to get the girl, he doesn't HAVE to get away happily, but he never seems to go anywhere at all.
For example, the "hell train" conversation with Leliel was kind of neat, but it ultimately feels empty. It's just talking to the audience about philosophical viewpoints and character traits that are blatantly obvious. It feels like the complete opposite of "show, don't tell." It's not good storytelling, at least as I see it (the show as a whole has this problem.)
And for that matter, Shinji's past seems way too obscured for his character to be even remotely interesting:
We know that his mother died when he was 3 and his father left him a year later. Then, he lived with his "teacher" (whom we never learn anything about) for 10 years. There never seems to be anything to go from. We pretty much learn nothing about him, aside from his personality traits.
And his reasoning basically boils down to "noone understands me", which just seems lazy to me.
There are several more things I could mention, but I'll stop there. Maybe I've missed the point, but I just didn't enjoy the show.