The best thing to do is find the OVA release End of Evangelion, which is the director's intended ending, watch episodes 1-24, then End of Evangelion. If it still doesn't make sense, get NGE: Death and Rebirth and watch it followed by End of Evangelion again.
Spoiler alert:
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With the indended ending from End of Evangelion, Shinji's father, Ikari Gendo, instead of being perhaps the record SoB in all of anime, is just another deeply flawed character, like every other character in the series (with the possible exception of Eva Unit 01).
Got them all. I gotta disagree. I’m nor religious about it but I found a lot of depth. I know some fans are insane about it.
When you pile all the actual religon/morality they weave into every part of that show, from the obvious angel refrences/Nephlim To the....
Spoiler
... Unit 1 as God/Mary in one being, I’d say it’s deeper than a lot out there.
See also the video game seriea Xenogears/Xenosaga. Great stuff!