The final scene
The closing scene is vague and highly interpretable, and has caused several controversies as to its possible meanings. In the scene, Shinji and Asuka have separated themselves from the collective human existence, apparently alone in the post-Third Impact world. There are indications that Shinji emerges first and considerably before Asuka does. Shinji has put up memorials to those he loved, and Misato's cross on her memorial has visibly rusted. Their interaction on the beach display a wide range of positive and negative human emotions. The world is irreversibly changed, however, and what happens afterwards is only hinted at.
Asuka's closing line, "気持&
90;" ("Kimochi warui.") likewise can be interpreted in a number of ways. It was translated on Manga's DVD as "How disgusting," but it can also be translated as "I feel unwell/terrible/sick," "What a disgusting feeling," "Feels bad," etc. This has caused much confusion among Western fans, though the true meaning of the line is unclear in the original Japanese as well. An episode of Anime Yawa, a Japanese show dedicated to anime, was broadcast on NHK's satellite TV 31 March 2005; it described this final line and its original meaning: initially the final line was written as "I'd never want to be killed by you of all men, absolutely not!" or "I'll never let you kill me." ( "Anta nankani korosareru nowa mappira yo!") but Anno was dissatisfied with all of Miyamura's (Asuka's seiyuu, Yuko Miyamura) renditions of this line. Eventually Anno, asked her a question which described what he was going for with this scene:
"Concerning the final line we adopted, I'm not sure whether I should say about it in fact. 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, 'I thought as much.'" 
Tiffany Grant, Asuka's English dub voice actress, says this:
The most widely circulated translation of the last line of EoE [End of Evangelion] is "I feel sick," but Amanda Winn Lee (voice of Rei Ayanami, who also directed EoE) said she asked several translators, and she felt "disgusting" was the most accurate adaptation. You could say she is disgusted with/sick of the situation or with Shinji himself. My favorite explanation though, is this one: My husband, Matt Greenfield, directed the TV series and is very familiar with the whole Eva franchise. Matt has said that although (Eva creator) Hideaki Anno seems to change his mind frequently about what various things mean in Eva, Anno once said that Asuka's comment about feeling "sick" was a reference to morning sickness. Now THAT gives ya something to think about, doesn't it! Of course, Anno is quite passionate about the idea that every person should decide for him or herself what Eva means to them.
There have been speculations that Asuka may now be an amalgamation of Asuka, Rei, and Misato because of her apparent red and brown eyes, the same eye colors as Rei's and Misato's (respectively). Further, she is wearing bandages that correspond to the physical damage she suffered during her last fight in Unit 02 (pierced left eye, injured right arm); these injuries mirror Rei's injuries seen in the opening episode of the original series. Furthermore, Rei had appeared to Shinji above the ocean of LCL in the previous scene. This theory was first proposed shortly after the movie was released, and was popular for some time. One point raised against this theory is that in this scene Asuka's eyes are actually their normal blue, and not a reddish-brown. A scan of the Cardass Wide Card for the scene in question, which reproduces the original cel used for it, shows that her eyes look somewhat grayish, but this is because of the color tones and lighting of the scene.
Another explanation of the scene that can also be derived from the explanation on the "ONE MORE FINAL: I need you." card is an affirmation of Shinji's choice to return to reality, and in doing so, separating himself from Asuka once more. His first impulse is to strangle her, to finish what he started during Instrumentality, but once he feels her caress (which is very similar to the one he received from his mother only moments before), he realizes what he's doing. He releases his grip and collapses as an emotionally broken little boy, which disgusts Asuka. This presents a more human response in showing Asuka's opinion over Shinji's behavior, but the act of caressing his cheek may represent a better connection between the two, since it deviates from Asuka's normal response to fight back or slap Shinji.
Despite the somber ending, there are clear statements that the results of Instrumentality are not permanent. Both Rei and Yui comfort Shinji and tell him that people can restore themselves to physical existence if they want to, depending on the strength within their hearts (the appearance of specters of Rei in a school girl uniform earlier in the film over dead or dying persons as well as living raises the question over whether they joined Instrumentality and could return). This being said, it is obvious that Asuka is one of the first persons to manifest herself back into reality. Another Evangelion trading card explains:
"In the sea of LCL, Shinji wished for a world with other people. He desired to meet them again, even if it meant he would be hurt and betrayed. And just as he had hoped / wanted, Asuka was present in the new world. Only Asuka was there beside him. The girl whom he had hurt, and who had been hurt by him. But even so, she was the one he had hoped/wished for...."