The biggest difference between Alex Smith and Colin Kaepernick is Kaepernick is not afraid to anticipate throws. He does not wait for confirmation that a wide receiver is open.
Smith has become so conservative, calculating and untrusting that he consciously waits for confirmation.
If a quarterback has to wait for confirmation before making the throw, it is too late.
Smith is like a pitcher who calculates his ERA on the mound in the middle of an inning.