Because in the end, John Watson is a good man. Not a great one, but a good one, and good men eventually attract very good women. Following nature's course, they may have children, begin working, building a life together... How much time do you think he will have for an eccentric great man who insists on dragging him all over God's green earth at the drop of a hat?

In the case of Jim Moriarty... He's fixated on you since you are, in the end, the only one who can match him in wits. I'm sure you've noticed, there aren't many men like the two of you in this world. Why on earth would he let you go when he may not meet another like you in his lifetime?

How confident are you that John won't eventually find a woman who compliments him perfectly?