No, they clearly cared for each other, but neither would admit it. Basically, Asuka wanted Shinji to come to her, but he was afraid of her. The kiss scene in episode 15 is a metaphor for their entire relationship: they kiss each other, she suffocates him, he's afraid to make a move, she's angry he didn't. They push each other away. In EOE he realizes the entirety of what happened between them AFTER SHE DIES. This is the scene where they talk, she says "no" and he chokes her, because he's mad at the way she (on the outside) rejected him. The next time he sees her is on the beach, very shortly after the choking scene in his head, so the first thing he does is choke her. There's nobody else around anymore (Asuka and Shinji were the first to return to human form after being turned to LCL), so Asuka's usual I-HAVE-TO-SHOW-EVERYONE-ELSE-THAT-I'M-THE-BEST personality is gone. She strokes his face, he realizes she isn't pushing him away like she was before, and he cries and lays on her. Her final line is just an ironic exclamation in response to what has happened in the world.