The name of the doctor
My theory: he did not change his name into a, as he said, promise, because he did or were something so bad in the past, but because of what he will do in the future!
We saw him and the Master as children looking into the Vortex, the ‘thing’, the hole, that shows it all. The past, the present and the possibilities of the future. He said “some go crazy!” like the Master may got.
What, if he and the Master saw a fixpoint in their future, when they will do or be or have to be something really bad? The Master keeps coming back to the Doctor. Wants to be with him, wants his wolrd with him, wants something we still don’t really know. The Doctor had the point in his life, when he said:
"ok, I can’t live with the knowlegde of my future. I can’t change it, but I can compensate it with good! I don’t want to be known for this after my life. So lets go and do the best out of the rest between. From now on, I will be the Doctor! Maybe in time and space I’ll find a place I can help! Where I can give hope and will be known as a good man! I’ll keep my name as a secret, until the bad things happen."
Maybe the rest of the family also knew, what will happen with him or because of him. Maybe his knowledge about the future made him that scared in the dark by night. He was “so lonley” as a child, cause the others segregated him and the Master because of their future.
Only Susan trusted in him, not even his wife and children could stand by him. So he took Susan with him to start his journey :)
I’m sorry for my english and it is hard to explain something in a foreign language :)
I would love to see a discussion or other theories :D