Indeed.
I think when the series ends Bay will have a more mother-daughter relationship with Regina, but let's face it, it's ALWAYS going to be complicated.
But I would imagine it would be if it was an adoption situation and the birth parents were introduced.
Bay is always going to see Kathryn and John as her parents, and she should; they raised her for sixteen years, but she grew inside of Regina and is Regina's biological daugher and therefore they will always be bonded. It's what makes it intricate and beautiful.