Kendrix wrote:that is such a good catch!
obviously the parallel is more explicit in ep 24 with the "You betrayed me!" line
I didn't spot THIs shot, but it showed up on twitter:SPOILER: Show
Obviously a very blatant visual parallel to the conversation between Shinji & Kaji in 2.0, perhaps underlining that they had a similar relationship.
I only just realized that Kaworu wasn't actually in those flashback scenes with Kaji.
Kaworu is just switching places with characters in Kaji's memories during the instrumentality. When Kaworu has the NERV commander suit on, he is taking Gendo's place in that memory and when he is in that red water purification facility memory, he is switching places with Shinji.