I am too one of many people, who think that Neon Genesis Evangelion was brilliant (what a coincidence!)!
I liked Neon Genesis Evangelion mostly because
all the characters (including 'minor' characters like Maya, Makoto or Keele) had complex and well-developed personalities. Neon Genesis Evangelion was the true masterpiece of Hideaki Anno!
However, when it comes to endings, I must say, that I liked movie ending much more then the series ending. IMHO, the series ending was too idolized, i.e. everything went peacefuly as it planed, humanity was 'complemented', and every person became god in his or her own mind - in his or her private Garden of Eden.
On the other hand, the movie shows the cruel and mercyless ending: because of one man's unwillingness to go with the 'perfect plan', and because of his desire to keep everything under his control, we are able to see one last battle for the future of humanity.
Being quite a grim person, I tend to dislike 'happy endings', prefering much more grim endings, as it was in the End of Evangelion, when Shinji wanting to be alone made Rei/Lilith devastate the Earth and proceed with the Third Impact. And afterwards, feeling guilt for what he had done, Shinji rejected Third Impact, forcing those few, who still had will to live on, to live in the devastated and lifeless world.
P.S.If you are fan of Neon Genesis Evangelion and enjoy reading fanfiction, I
really advice you to read Regina's fanfic "Once begun it cannot be undone"! Even though the first chapter may seem to be a bit unclear and complicated for you, in the following chapters the story will begin unveiling itself, becoming just fantastic!