After he rejects it though, it’s stated that anyone with a strong enough desire/will to return can also reject it, hence Asuka coming back after him. You could imagine that happens to others, or you could imagine a new Adam and Eve scenario, both of which are intriguing in their own rights.

You’re totally right about the plot structure going semi-haywire (villains left unconfronted/discovered, and never really getting the kind of perfect/complete breakdown of their methods & motivations we rationally desire) - BUT - that’s from the perspective that seeks control (total knowledge) or seeks to dive in to “escapist fantasy” completely, and I think that in fact one of the most powerful things NGE as a franchise has to say is on the rejection of complete escapism! Both the original show and the rebuilt series end by showing the real (non-anime) world, and I don’t think that’s an accident. Shinji’s choice is ultimately one between “comfortable” fantasy of total ego dissolution, and (the sometimes harsh) reality, where the only way to connect with others involves making yourself vulnerable.

:)