I think i may know what it all means... spoilers

First things first, what i'm about to say could be BS so take this with a grain of salt. OK...here is my theory, i think that Hideaki Anno was right, there is no "hidden meaning" all of this, because everything is in plain sight. In EOE Shinji accepts instrumentality for a little bit. In instrumentality all souls or "released" and returned to their origin. Everyone has a change of personality and people who were dead are alive for example Shinji's mother. In other words instrumentality is NOT reality.Well i think Shinji represents otakus...kind of, let me explain. Otaku is a word that refers to someone who is obsessed with Anime or/and Manga, because of their obsession they tend to fantasize or spend most of their time watching anime or/and read manga, and by doing so they are stuck inside a realm where...well it feels um i cant seem to think of a good word but um "accepted" or...yes happy. OK now back to Shinji, in the last Evangelion episode Shinji is in a place where he feels accepted and actually pretty happy and living a normal life, even his mother is alive. Hopefully you see what im trying tell you. So anyways Shinji is kind of like an otaku, he escaped reality to a place where its happy. BUT later on we see a confusing scene in the last episode where a bunch of people are congratulating him. What for? Well back to the movie. In the movie Shinji rejects instrumentality and now he is in the real world he's in reality. He rejected instrumentality, i think, because he finally realised that in real life there will always be obstacles in your way and...well running away from them into a fake fantasy where everything is perfect is just going to delay the inevitable. So he rejects instrumentality. So i think that was what they were congratulating him for in the last episode. So then in the movie giant-naked- winged-angel-Lilith-goddess-Rei-Ayanami-thingy said people will leave instrumentality if they truly want to, in other words, those people are also experiencing there own perfect fantasy world. So to quickly rap this all up because this is getting a bit lengthy, the whole was a message to otakus...no the audience in general to not to live in their own fantasy world where everything is perfect and the way they want it, but to go outside meat new people, enjoy life, and most importantly face your fears and overcome the obstacles block your way.

In conclusion i wish i had more time to explain more, im probably going to edit later on to this but for right now im sleepy and i have school tomorrow so maybe after school, but for right this will have to do.