UrsusArctos: This is all stuff we'll see in full in Episode 21. This traumatic event - the loss of Yui in the Contact Experiment - appears to have been burned into little Shinji's memory and was poking at his subconscious all this time. Evangelion 3.0 explains away Shinji's non-memory of the Eva or Yui's disappearance using stuff like memory modification. Even with the significant changes in settei, 3.0's take on it seems rather more hokey than the simple forgetting that we get in Episodes 20 and 21.
