To quote Legandary:
Gendo: The true Evangelion...
Gendo: Its completion will be ushered in by the current body containing Unit-01.
Fuyutsuki: The Mark-06, isn't it?
Fuyutsuki: This means what they are trying to create is not a false god, but a true god at last?
Gendo: Yes. We must hasten the awakening of Unit-01.
Now this goes into the sequel theory again but i took it as... the "real" evangelion, unit 01, is inside the body/armour of unit (mark) 6 (so having the original series unit 01 from the moon or in space, wherever from EoE).
So to quicken the awakening of it, the events in 2.0 occur, bringing not only Mark/Unit-6 down (the true evangelion unit 01) for them, but what Azathoth earlier wrote about nebuchadnezzar - Kaworu, son of the gods etc, to appear out of nowhere(plus the whole real god/fake god stuff).
Then this leaves the key to be used - on the real original eva 01 perhaps?
Bit of a fan-wank, and probably has holes in it i'm unaware of due to me being rusty in all things eva, but it seems quite convenient to me!