Despite the fact NGE uses many Freudian terms, it is much more rich in Jungian imagery, and the dynamics of the show resonate well with Jung's model of the psyche. This is partly because Freud offers no satisfactory explanation for the mysterious, paradoxical and religious elements of the human mind (elements which make Eva so intriguing). In addition, Freudian psychology is phallocentric, focusing on issues dealing with the Father, while Jungian psychology is better suited to focus on issues dealing with the Mother in both its archetypal and biological meanings.
NGE is very much like a concretized dream, or a drawn out fairy tale and can be analyzed as such. To simplify this, we can regard the current situation of NGE - a post apocalyptic world - as a representation of the state of the psyche. Try to imagine the psyche as a system striving towards homeostasis. There are set levels and balances that are optimal for a system's performance, and when there are imbalances, the result is illness, or a malfunctioning within the system. So usually there is a sort of regulatory function integral to the system to ensure things do not go awry.
First and foremost, we can regard Jung's archetype of the Self as this integral, regulatory function. The Self is one of Jung's more confusing archetypes, but for our purposes, we'll simplify it, and align the Self with the unconscious mind and the totality of the psyche.
If we use the human body as an analogy for the psyche, you can say that the regulation of homeostasis is done mostly without your conscious intervention (controlling endocrine levels, growth rate etc). If needed, your body can prompt you to aid in any regulation (feeling thirsty when you are dehydrated, discomfort if you are too hot or cold). The Self archetype acts very much in the same way. For the most part, it functions in the background without you noticing it until you're prompted to act (feeling bored? Got to watch some anime! ^_~).
Now, if the Self cannot resolve any imbalances, it will compromise in an attempt to maintain the integrity of the psyche. To bring back the body analogy, this is like when the body decides to withdraw blood flow to the extremities in the case of exposure to extreme cold. This act may damage the tissue of the extremities, but maintaining your core temperature, making sure you survive with or without frostbite, is the body's first goal. And just to let you know that something is wrong and that conscious intervention is needed, the Self and the body will often use pain as a means to get your attention.
Taken from this perspective, it is obvious NGE's setting of tenuous human survival and attacking angels indicates a deep complex which must be resolved. Whatever is imbalanced or marginalized in the psyche must be brought to consciousness and fully integrated. To discover the complexes, we begin with looking at any imbalances in the characters.
Although issues of the Father arise (in the case of Misato's revenge and ambivalent attitude to her father and especially Shinji's distant relationship with Gendou), examination of all the characters reveal a much deeper loss: the Mother. All the children of the Second Impact seem to be mother-less. The adults are not much better off, Ritsuko is betrayed by her mother (in computer form), Misato's is practically never mentioned, Fuyutsuki's attachment to Yui suggests a longing for the mother and Gendou is just plain creepy when it comes to women.
So let's examine the meaning of the Mother complex, how this relates to the connection between the Jungian archetypes of the ego and the Self, and how NGE has managed to take threads from science fiction, Christian mythology, psychology and weave them together to create an interesting tale pertinent to contemporary society. Please continue here.