I've always thought that full range of motion is always best. With squats and other leg pressing movements it should be ass to ankles or as close to it as possible. Apparently that doesn't seem to be the case. At 6'2" I can't count the number of times I've tweaked my back doing full squats -- not to mention how horribly uncomfortable it is.
Measuring muscle activation using EMG it appears that parallel, 90 degree angle, stimulates the quads the most and that the most effective exercise is the hack squat. Something the Coach will not want to hear and won't believe no matter what science objectively measures.
http://suppversity.blogspot.com/search?q=how+deep+squats"Turns out the hack squat is the most effective exercise. In that, going deep
(50° knee angle) is only slightly more taxing on the quads than the standard
and much safer 90° knee angle."
"What I consider of particular importance is that both in the case of the hack- as well as in the case of the "standard" barbell squat, going beyond parallel (knee angle <70°) is not worth the increased risk of injury (cf. figure 2)."