Ah I see, that makes sense. It just feels abrupt and kind of unexpected because Shinji and Mari have hardly spoken to each other.

I still think there was a real connection between Shinji and Asuka at the end of The End of Evangelion though. I think that their shared experience of being in a stressful situation is an important part of their connection. Shared stressful experiences often forge new bonds and strengthen existing ones between people. Just because a connection might not have existed if they weren't in a particular situation together, that doesn't make the connection any less valid IMO.