Shinji doesn’t end up with anyone. Mari is there with him at the train station and leads him out because she promised Asuka that she would bring him back. We also know that Mari is aware of Asuka’s feelings for Shinji and keeps trying to get her to it to them thanks to Evangelion 3.0: (-120min.) plus her comments in 3.0 + 1.0. We’re also shown how strong Asuka’s feelings are for Shinji in (-120min.).

When Asuka tells Shinji that she liked him but she grew up first, she is saying this for her own sake and trying to give herself some closure. , she thought that her and Mari were going on a suicide mission. She didn’t expect to return. However, we know from Evangelion 3.0: (-120min.) that she still has very strong feelings for Shinji. Asuka recites a poem about a woman who longs for her husband to return from afar. When Mari teases her about her feelings and tries to get her to acknowledge them, the first memory that comes to Asuka is Shinji smiling and giving her the bento.

Shinji, for his part, also thought that he was going on a suicide mission and didn’t expect to return. His confession to Asuka that he also liked her was an attempt to give himself some closure and probably to make Asuka feel better that her feelings weren’t unrequited. His “Goodbye Asuka” is a call back to earlier in the movie when Hikari tells Rei that “Goodbye is what we say when we hope to see the other person again.”

Mari and Shinji are alone on the platform representing them in the anti-universe. We see that the opposite platform is full of people. That’s everyone in the real world. It’s also interesting to note that Shinji and Asuka are both sitting on the same seat. Mari then frees him from the curse of the Eva by removing the choker. She also pockets it instead of tossing it away. She then takes Shinji’s hand and leads him out of the station (the anti-universe) and into the real world this fulfilling her promise to Asuka. What happens after this is up the our imagination.