No clarification. The ending of both the series and the movie were like Kafka's the Trial: the come out of no-where, suggesting that there's meaning to be found, but ultimately conclude nothing. We're left on a beach with Asuka strangled-and-yet-not-dead, Shinji crying softly, a vision of Rei appearing randomly over the Sea of LCL, and the wonderful cockslap last words of "I feel sick." HWHAAA? Thank God for Wikipedia & eva-geeks.org; otherwise I'd be adrift.

The religious symbolism being kind of hammered in wherever it fits, even though it makes little to no sense.

Lots and lots about what's bad in humanity, but very little ideas of how to fix anything.

Not enough clarification on universe mechanics. Specifically, the workings of souls, AT Fields, Angels, Seeds of Life, the Dead Sea Scrolls, and even humans.