I did notice something while watching the GJ video, specifically the shot of Sakura:
This scene represents someone waking up on a bed, and directly references Shinji's "birth" from Eva01's juices at the beginning of 3.0. Could this be the birth of a new Shinji?To put a timeline on this:
Asuka, Rei, and Shinji are walking through the wasteland
Shinji sits down to pout (per Peaceful Times)
Asuka puts foot to head, pushes him down and continues walking
ReiQ brings Shinji back and they proceed toward NeoNerv HQ
Asuka arrives back at WILLE HQ with no Shinji or Rei
Misato decides to generate a new Shinji so that they can ask him to pilot Eva01
Tells him the truth about everything this time and lets him decide on his actions
Perhaps Eva13 vs Eva01 is actually...Shinji vs Shinji?!
One who is ignorant and pushed to the brink of insanity, another who is embraced and pushed to the brink of greatness?!