Preface:
27 years old, 5'7, 145lbs, have been doing calisthenics for a few years now. I've sprained my ankles in sports a few times over the years, so they're not 100%. I don't believe there is anything major that is structurally impeding their flexibility. All of my ankle sprains occurred from rolling the ankle through inversion.
Currently I'm on a mission to perfect a barefoot deep squat, without using my arms for counter balance. Getting my heels down while in deep squat has always been an issue for me. I can manage with sneakers on or while holding my arms out in front to balance, but this is far from ideal and I know I can do better.
I noticed that while in a deep squat, trying to achieve an unassisted position with my heels on the ground, my ankles begin to exhibit eversion to the point of inside ankle pain, which feels like high tension in the medial ligament.
Thinking this was a dorsiflexion issue, I've been working on flexibility in the hamstrings, calves, and achilles, and have even entertained the idea that my femur is just too long to accommodate this feat.
Rummaging through search results today, I discovered following post from 2009, in which Naterman describes a neural pattern correction involving wall squats: