I took it to mean that Shinji is constantly the most troublesome of the bunch, and that Kaworu has been chilling out on the moon for a while now watching the events of the movie happen.
After watching the movie I went back to Wikipedia to brush up on the Eva lore and shit, and came away with a better understanding I think. You can strip away all the semi-philosophical existentialism and still find a neat sci-fi story, and even some of the psychoanalytical stuff has its value. What I loved the most about the show was how they handled the Angels. They were all pretty neat, mostly unique, and you get a real sense of "Us vs. Them" mentality when you see shit go down. And it helps to see that element going into the final movies, when you discover that Humans are an angel too, just different from the ones born from Adam, set against one another in some sort of bizarre cosmic existential tournament Rebuild is taking these encounters and spiffing them up, and keeping turbo mindfucks to a minimum.
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