Yeah, the end of NGE gets props for being "artsy" and "different" but a lot (almost all) of the religious symbolism and weird stuff was thrown in simply because it was weird and made it look more complex than it really was.
In the TV series, the studio flat-out ran out of money and couldn't do the last episodes which were supposed to show the grand final merging of humanity. They instead had to use static images and re-used scenes because that's how broke they were. The point of the last two episodes is to show that Shinji doesn't really want to join everyone and comes to terms living as a separate person on his own. It's supposed to show his thoughts as the grand instrumentality whatchamacallit takes place since they couldn't animate the actual events.
In the movie however:
Essentially, everyone gets turned to goo and merged together to create the FINAL END STATE OF HUMAN EVOLUTION (as if yellow goo could be called that) and it's supposed to create a world in which everyone is happy and understands each other since everyone is now all joined together as yellow goo. Shinji's supposed to be happy in this world, but he decides that he doesn't like it and realizes that such a world might be peaceful but it's lacking in hope and joy. He chooses to emerge from the sea of goo (which is a choice all humans have, but it implies that most will never take it) to start a better world in which he might be personally unhappy but might make the world a better place for future generations. Except that it probably won't because HAVE YOU SEE WHAT IS LEFT OF THE WORLD AFTER THE FILM!? It's a MESS! No one wants to live in a world in which the sea has been turned to yellow-people-goo and giant frickin crucifixes litter the landscape!