Much of his motivations are still cloudy even at the end of the series. One wonders even to his end what lies behind those glasses, and the truth about the man that hides in the darkness of the crimson leaf.
The final piece of the puzzle reveals itself in the movie End of Evangelion. As Ikari Gendou brings Ayanami Rei III to Lilith to initiate Third Impact, Dr. Akagi Ritsuko, whom he had an affair with, steps in their way. She raises a gun, and Gendou protects Rei. After mentally combating her, she lowers it.
My point to this page:
What were the last words Akagi Ritsuko heard from the man know as Ikari Gendou?
I'm leaving this open to debate, so mail me with your comments. I'll start posting once I get some.