From the Platinum Collection booklets:
Thus, the story of Eva would branch into two stories with the diverging point being the end of Episode Twenty-Four "The Final Messenger." The two stories each unfold differently and arrive at their own climaxes.
It is not that one is the complete version and the other is incomplete. Just like the multiple endings of a game, two different endings were prepared for one story.
Gendo uses Rei to execute the Human Instrumentality Project and the complementation of man begins.
Gendo says, “All souls will become one and find eternal peace”. His Instrumentality Project must have been for all human souls to be combined as one and to compensate each other for what they have been deprived of. In the story that follows from Episode 25 “Air” to Episode 26 “A Pure Heart For You”, he was not able to execute the scenario he had drawn up. It may be that it was in Episode Twenty-Five and Episode Twenty-Six that his wish actually came true.
The moment that Shinji gains conviction that it is okay for him to be there, the background changes, and the blue Earth spreads beneath his feet. However, there are no continents on this Earth, and it is covered by a gigantic coral reef. It seems this is the Earth that has been transfigured by the Instrumentality Project.
It is left for the audience to decide whether this ending is the Best Ending or the Bad Ending.
From an interview:
Hayashibara: So there will be two episode 25s.
Anno: Right, it will be a multi-ending.
Hayashibara: So, a dual... ah, a multi-ending. After episode 24 the endings will diverge.
Anno: Right.
Hayashibara: There will be two of them.
Anno: There will be two of them.
Hayashibara: Ah, two endings.
Anno: Yes.
Hayashibara: In terms of gaming - is it called a simulation game? What do you call it? The ending for that [particular] self changes as you go on [through the game].
Anno: Right, a multi-ending [game].