Gendo finally spills what was probably the worst kept secret in the whole story: he doesn't like Shinji. In fact he hates him. Hates him to the very core. That Yui, understandably as a mother, would shower affection on Shinji, didn't fit well with Gendo. Yet again, like Asuka, Shinji comes to the realisation that his birth wasn't welcomed by one of his very own. Predictably because it's the final time they'll ever meet, the father also tells his son to join his crusade. The crusade to make him into a God so that he never loses anything again.
Gendo, in short, is an absolutely miserable human being. Unable to face the loss of his loved one, he's hell bent on turning the rules for himself, rather than accepting them as any other human being. In his quest for getting back to the one he loved, he has ironically severed several other relationships, alienated his own son, used people for his own causes and then leaving them in the cold.
' I want to become God, so that I won't lose anything'..
One of the pet themes of Eva is how the characters deal with personal losses, and Gendo's reasons here aren't meant to be viewed in a sympathetic light.
I would've liked the manga to explore more on Gendo's past, the guy he was before he met Yui. I guess the manga missed a trick there.