I don't think that was Shinji (just a theory)
I don't think that this is actually Shinji, I think Shinji is still trapped inside the eva some where. In the beginning when Shinji walks on the bridge of the Wunder Misato and Ristsuko say some very strange things. I remember heading his DNA is almost 100% identical to the third and something about his teeth have developed properly-I don't remember that line correctly-so I really don't think this is Shinji. I think this might just be a reproduction of Shinji, think of how Rei is a vessel, this might be the same deal instead this Shinji has all the memories of old Shinji. I might be completely wrong but the real Shinji might still be such in that cross that fell to earth.
I will not fear, fear is the mind killer