There are many different types of aids to help make a shoe more comfortable even after "breaking them in," and can be purchased at shoe stores, large retailers, and some drugstores. These include special small gel pads for the balls of the feet, heel inserts to help minimize chafing at the back of the shoe and rough patches to glue onto the bottom of a slick sole, affording you better traction.
Consider a lower or more comfortable style. Choose a thicker and more stable heel like a platform, wedge, or chunky heel to provide more support and weight distribution. Shy away from pointed-toe styles if you have wide feet or toes, opting for round or almond-shaped instead. You can also buy heeled boots or heels with ankle straps to help support your ankles.