The material, while drawing on Christian imagery, owes most of its themes to Jewish mythology and lore. On the philosophical level, the story is a meditation on Genesis 2:18: "It is not good that the man should be alone;" and so the Human Instrumentality Project--man's effort to finish God's statement: "I will make him a helper fit for him," which is ultimately fulfilled at the very end of End of Evangelion. The key phrase here is man's effort, as this is what Evangelion is on the micro level.
Have you heard the legends surrounding the interspecies drama of the Nephilim? That's along the lines of Evangelion's setting, except it is a similar legend of Lilith. The lore tells how Lilith, Adam's first wife, who left her husband and consorted with demon Samael, begetting a myriad of demonic offspring, the lilin. The legends continue that God sent three angels to bid Lilith return to Adam; were she to refuse, one hundred of her offspring would die each day. In Evangelion, the humans are identified as lilin--which would explain the attacks of the angels. The EVAs, it is revealed share DNA similar to people (or, rather, the lilin), if we were to seek an analogue in the lore, the EVAs are golems, dust of the ground (the stuff of Adam) raised into an animated being. I hesitate to say they are living because, according the the lore, golems cannot be alive, as only the Lord gives life. Essentially, Evangelion is the story of Lilith's offspring fighting (and prevailing over) the angels God sends to kill them for their mother's rebellion, an ironic twist on the doctrine of Original Sin.
As another pointed out, the series contains a lot of ideas thrown into a blender. Sure, I get that (the Dead Sea Scrolls, for instance, have no semblance to the real-life DSS), but the overall themes are right on the mark for the legendary stories.
