This was my take on the dad plot. He told Gene he didn't want to fight with him anymore. When he got knocked back to 1973, it sort of integrated history from the computer with his own memories (swiss cheese for brains from Quantum Leap theory). He went to sleep fighting with his dad and had those "demons" in his brain to work out. So, he created an evil dad that he had to defeat. I was guessing that this ending was at least thought of during the entire series and they just had to shoot it when they learned of the cancellation. Would they really be doing 3 seasons and not know where it was going? They wouldn't be able to put in the clues if so. Sort of like Lost - they knew from the beginning how the ending would be. They just have to add great arcs in storylines to get there.