At times it was difficult for John to even look at Adam.
He would find himself looking into to his youngest son's face and only seeing the shadow of his last love, not the boy himself. Sometimes Adam would turn his face just so or an expression would cross his features and all John could see was Kate. He saw her soft cheeks or her wise eyes or the wry smile that seemed to permanently live on her lips. Each time he would catch that momentary glimpse a new hole would be torn in his soul and he would struggle to try to keep himself from drowning in the feelings that threatened to overtake him.
It's not as though he wasn't used to seeing the remnants of his love written on his children's faces. There were so many, many times throughout the years that Dean would smile just like Mary or Sam would raise an eyebrow in her same skeptical way. Each time he caught a glimpse of Mary in his boys, John's heart would twist and his stomach would clench as he felt the pain of her loss as fresh as the first moment.
But it was different with Adam. John found himself taking great pains not to apologize to his son each time he recognized his mother in him. As if he could beg her for the forgiveness he knew he did not deserve. He wished he could plead with her to absolve himself of the endless guilt he felt when he looked at Adam.
Because if Kate Milligan had never met John Winchester…
When he could stand to look at the boy, John would comfort himself with the thought that Kate would want Adam to be safe and that training him in the way of the hunters would do just that. The boy was half Winchester after all and the supernatural evil of the world was bound to be drawn to him.
At those times when John had to look away, had to grit his teeth and stare hard into his papers or the road in front of him, he could offer himself no comfort. In those moments he could not rationalize away the thought that Adam was just a boy, a child, who by all rights should have grown up with his mother and had a normal life. John was wise enough to realize that no matter how much Mary had wanted it, no matter how much Sam wanted it now, there was likely no 'normal' life for Sam or Dean. John had never intended to be a hunter, but Mary was a hunter legacy and from what John knew of his own terrible Winchester luck, his older sons would never stand a chance of out running their destiny. It was all John could do now to prepare them for it.
At most John could hope that Adam never noticed the difficulty he sometimes had, but he often feared the boy was too much like his mother and saw right through him. Kate was always like that, able to walk through John's tried and true emotional defenses, able to see straight into the depth of him, whether John wanted her to or not. Kate was so young when they met, but John had often told her she had an old soul. She knew more about the world, more about people, then anyone her age should. And it was clear the more time that John spent with Adam that he had inherited this trait as well. There were times when John would look up to see Adam looking at him, in just that same way Kate had. It had been John's instinct to snap at her when she did this and true to her form she would just wryly smile at him and slowly look away, back to whatever it was she was doing. More than once John had snapped at Adam the same way when he found the boy staring. But unlike his mother, Adam wouldn't offer John an amused knowing smile, instead the 12 year old would continue to stare, watching John carefully, quietly absorbing his father before slowly looking away. While Kate's stare had warmed him, Adam's unnerved him, like the boy was looking for answers to questions that he didn't yet have the courage to ask.
When John could quiet his mind, stop thinking about the next hunt or the past losses, he would look at each of his boys and let himself feel, if only briefly, the deep aching pain that looking into each of their faces would bring to him. He would clench his fists, bite his tongue and send a promise up to their mothers that he would do better and be better for them. John Winchester knew more than anyone that the road to hell was paved with more than good intentions.