It almost feels like Eva 01/Yui is trying to stop him from going back, well it's obvious that is what is happening. But I wonder if it's her own will or the Angel that 01 ate. If that is indeed a physical manifestation of Yui, she does indeed look like Rei, even more so than in the anime. I'm guessing Gendo had a momentary lapse and saw Yui in Rei and it seems like Rei is having an effect on what is going on the Eva?