In my experience, the number one pre-cursor to an overuse throwing injury is what I call "wing," where the elbow lifts above the ball to initiate the throwing motion. This is debated extensively in baseball pitching mechanics, and while the world of quarterback mechanics isn't quite as publicized the issue is still equally important.
Above you can see two clear examples of the wing (you can ignore the circle around the foot, that was from a different illustration). In both pictures, the throwing motion is being initiated by the elbow being raised up above the level of the ball and shoulder. This is a terrible position for the shoulder in general, but even more so when it's to be followed by as strong a level as the shoulder is capable of. This motion tends to pinch or create an impingement at the rotator cuff, as well lead to labrum issues. That's not to say that all quarterbacks with this flaw get hurt - some folks are just genetically built differently and have more space in their shoulder anatomy and get away with the flaw (see: Michael Vick). However, it's definitely not the model to copy and really should be avoided all together.
What we want to see is a quarterback who goes straight to what I call the "90/90" position, which is a 90 degree angle between the body and upper arm, and 90 degree angle between the upper arm and forearm. Pretty much every quarterback hits this position during their motion. The issue is how they get there and where they go from it. We must avoid letting the elbow wing up to get to 90/90. Instead, push the ball up and move the body forwards to hit this spot. This allows the smaller scapula stabilizing muscles to engage, prevents any impingement in the shoulder, and also helps create velocity, accuracy, and consistency.
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