You see the thing is Every time the Doctor regenerates he does not just change his face he becomes a completely different man, his feelings change. This is shown best with Rose as when she is with 9 they are best friends but when he regenerates he becomes a younger man with different tastes and then develops the feeling of love for Rose. So when the Doctor regenerates it is like he has just passed his title and memories on to his Son from his deathbed as he is about to become a new person not at all as he was before!