If you get someone who squats with average depth to squat ATG with the same weight, they'll likely find themselves stuck trying to squat back up. That's pretty obvious though. I can squat considerably more if I only hit parallel.
Having said that, I don't think there is a better, worse, wrong or right way. It depends on what sport you practise. Sprinters/jumpers require extreme strength in the end part of the ROM, so it's not at all uncommon for them to do partial squats. Powerlifters obviously have to meet certain depths, and going any lower isn't necessary for them. Olympic lifters are going to benefit from ATG. Etc.