The use of Christian symbolism as nothing more than an aesthetic is somewhat common is Japanese fiction. I wouldn’t say it made no sense though.
The bad guys say humanity is fundamentally incapable of opening up to each other. Shinji proves that it can be done and is worth pursuing, although it is fundamentally difficult. He discovers acceptance of himself through his connections with his peers. He acknowledges that everyone must go through life at a pace they don’t get to choose, and that the inevitably of death doesn’t erase the meaning of existence.
The bad guys say humanity is fundamentally incapable of opening up to each other. Shinji proves that it can be done and is worth pursuing, although it is fundamentally difficult. He discovers acceptance of himself through his connections with his peers. He acknowledges that everyone must go through life at a pace they don’t get to choose, and that the inevitably of death doesn’t erase the meaning of existence.