In the final stage, none of the cast knows each other. None of that "would you like to become one with me", return-to-the-womb stuff is included. The world has been remade, but it's not an escapist remake. It's more of an inevitable evolution, a sign that the world is as always undergoing dynamic changes to the point of even fully shadowing the past (no one knows what the "relics" are) from which the present was born. Shinji still has his troubles, and as seen from the audience's POV of knowing the former cast, he has to face them alone. If he wants to make friends and relationships he has to build them himself. The past characters are just that: in the past. Asuka doesn't know him and probably won't ever see him again. If they do meet again the chances of them getting together are slim. Kensuke may or not become his friend. The important thing is that Shinji retains a life of opportunities that SEELE's scenario would have denied him and everyone else, because when he expressed his wish to Rei during Instrumentality to "hold her hand" he was really expressing the desire to continue living in a world of Selves and Others.
Probably because of the wintry setting, this ending reminds me of Nietzsche's poem "Vereinsamt" (Lone). However, in both this poem and in the final stage, there is the common image of alienation from the past serving as introduction to an uncertain future. This exists in the final scene of EoE as well. I think it fits the spirit of NGE (and especially the manga) nicely.
The whole manga was somewhat more cliched than the anime. We have to see the ending in its context.