ankles, ankles, ankles. my squat was terrible (shallow and weak - i couldn't even get down on my haunches and asian-squat properly) and i blamed hips, hip flexors, knees, hams and glutes, you name it. in the end, by far the biggest factor for me was my ankles. getting ankle mobility made everything else just fall into place. i still have occasional SI joint pain and my hip flexors still click and pop over my pelvis all the time but the mobility from hip to ankle is dramatically improved.