https://drive.google.com/open?id=0B4m6i91y3PypZEF1VTlmSE0ydWM
I re-watched the scene and it was weird because it seems like they went out of their way to set up the rainbow shot . Like they show the sunlight go into the water/beaker thing for the rainbow. I felt like that was a lot of effort for something so random so I started thinking about it .That scene is reminiscent of the final scene between Asuka and Shinji. The way Shinji is over Rei is similar to how Shinji is over Asuka. And remember how Asuka says disgusting at the very end. Well in later episodes I believe when Rei thinks back to this moment between her and Shinji she say's that she was "Disgusted" at the time.(If I'm worng let me know talking from memeory)
Now rainbows are a symbols of destruction in Christianity because the rainbow was God's way of saying "I'll never flood the world again". Well maybe the rainbow is meant to connect to the final scene where there is a literal kind of destruction of mankind. The rainbow was probably a very subtle way of either foreshadowing and/or a subtle way of being stylistically repetitive(aesthetic=repetition in this case) with the two scenes. Evangelion loves to be repetitive with it's imagery and story. I know I may be over thinking it but I thought it was worth/interesting enough of a topic for sharing.
Sorry trying to add image but cant get it to work, link is there though.
