I don't see what the mystery is. Michael went through an epiphany. Part of that was his attempt to make amends. We don't know when the epiphiny started. We don't know when the kids' "education" that Michael referred to began. Again, as part of the epiphany, Michael wanted to make amends and gave up at least some of his custody to Kay. Sure, as the kids got older they became assertive wanting to see their mother freely and expressing a desire to live with her perhaps. Tony comes to know that his father murdered his uncle. When? We don't know. That may have influenced Tony. Mary, as a female, naturallly wanted her mother.