I think the best argument in favor of the deep squat are the o-lifters. They lift huge and extremely flexible and atheletic. When you see them do the real deep squat clean, you can see how masterful a movement it is. And I second the anecdotal evidence that stopping at parallel is harder on the knee.
Sadly, my natural squat was trained out of me through years of catching in little league, on my toes. Re-learning in process…