Defenses have probably decided to treat Alex like other running QBs who's legs are a stronger weapon than their arm. Make him beat defenses passing the ball from the pocket like they did with Vick etc.
Force Andy and Alex to go deep, which neither prefer to do. Every chance Reid gets he will go with the short stuff. Alex Smith won't go off Andy's dink/dunk script and generally avoids risk and takes the safer throw.
Defenses know this and are keeping Alex Smith in the pocket and cover the short stuff.
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