I don't know if this already came up, but remember that story about how Anno wasn't satisfied with the last line: http://wiki.evageeks.org/Statements_by_Evangelion_Staff#Interview_with_Yuko_Miyamura_.28BS_AnimeYAWA.29
I try not to use outside evidence for interpretations, but I always thought this line helped frame analysis of the final scene:
At last Anno asked me "Miyamura, just imagine you are sleeping in your bed and a stranger sneaks into your room. He can rape you anytime as you are asleep but he doesn't. Instead, he masturbates looking at you, when you wake up and know what he did to you. What do you think you would say?" I had been thinking he was a strange man, but at that moment I felt disgusting. So I told him that I thought "Disgusting". And then he sighed and said "... thought as much." He said. " I thought as much. "
The whole set up where "violator" does something criminal, but not without first revealing some deeper intentions, reminds me of another story: A women was held up at knife-point by a rapist. He told her politely what was going to happen, and asked for her permission to put on a condom. She accepts, and he asks her to wait a patiently as he puts it on. Its alleged that this women was more traumatized by his manner than by the actual physical rape itself. Why was this man being polite? What reason did he have to put on a condom? Did he have aids, some disease, some history, and forced into a desperate situation?
The victims in both stories are confronted with "otherness," the exposure to another conscious agent, another person's truth/reality (the kind explained in EoTV). In Anno's story, the choice he gives to the victim is of two things: to acknowledge otherness, or to reject it. To me, this is the choice presented throughout the whole series, whether to connect with others or reject them. In the final scene, after all that HIP intervention, we see Shinji and Asuka given this choice again as a final test. To each other, they are the ultimate "otherness."
So did they accept or reject? I think they accept. I read the gestures of this scene allegorically, rather than practically. The roles are reversed: Shinji is violent and active, Asuka submitting and passive. They are behaving unlike they would before, expressing themselves in ways that were normally repressed. Shinji's strangling, and Asuka's passiveness and tender caress, are gestures of vulnerability. Asuka is acknowledging Shinji's otherness in her caress. Shinji, realizing this, accepts Asuka as well and releases her, taken aback, overwhelmed. They reach an understanding, make a connection, and pass the test.
Just for completeness: After the strangle-caress exchange, it seems like they revert back to their normal selves. Shinji is weeping and Asuka delivers her line. So what about the line? If the above story is true, Anno wasn't exactly satisfied with "kimochi warui," as it does seem like a rejection of his choice. Good thing its ambiguous enough. If we see the reactions after the strangle-caress as a moment of gratitude, a display of their normal selves, it doesn't contradict. The incarnation is complete, and we have expressed in this scene the whole of each other's individuality in full acceptance.