You're ignoring perhaps the most iconic Eva scene:
Instrumentality allowed Asuka and Shinji to completely expose themselves to each other. So much of the final episode is dedicated to them and its because of the message that wants to be portrayed as well as building the final scene.
The scene has been interpreted in many ways. My interpretation is Shinji not being able to differentiate fantasy (instrumentality) and reality. He has fantasies of asserting himself, especially to Asuka as she often (rightly so) talks about his cowardice and this is shown when he strangles her in fantasy and there's no response. Perhaps Shinji wanted to confirm he was in reality and not a fantasy and the way the scene plays confirms the difference between one's reality and fantasy.
Asuka responds, not with violence, but by caressing his face. She has finally accepted her "flaws" and through such an understanding is able to understand/show care towards Shinji. Asuka showing such care, awakens Shinji from his confusion and he starts crying when he realises what he has caused and what he was just about to do. Asuka's response is "How disgusting". Again something that is very open ended. Is she referring to Shinji's actions and what he had to do just to come to terms with himself or is she referring to herself, and how she now feels affection towards Shinji, or is she referring to how they have both exposed their deepest secrets to each other? The conclusion is still the same either way though.