I don't think it's really the ankles... for a pistol to be successful, and I know this because I can compare my left and right legs (I can deep pistol squat pretty easily with my left leg and I can barely get to parallel on my right), it's important to be able to "reach" the glutes and lower abs and to stabilize that pelvis.
On my right leg it's usually a lack of glute/posterior chain control/recruitment that I have that prevents me from getting all the way down, plus the lack of strength.