The NFL discusses certain things with players in terms of injury prevention. IMO they should also include in this some information on how to avoid shoulder separations. Especially to QBs as this happens to them more often it seems.
Essentially it would mean telling them to try to twist or roll slightly at the last second before hitting the ground so as to avoid landing squarely on the side of the shoulder with the weight of another player on them. This is the textbook means for acquiring a separation. It's usually the same type of impact, which to some degree can be avoided if the right (small) movements are made. Brady probably just got lucky in not landing at quite the angle that would've led to separation.
In addition, in Brady's case i'd have him wearing knee braces for the foreseeable future. They curtail mobility but the potential benefit outweighs the drawbacks, in his case.
