I think the greatest difference between A. S. Johnston, J. E. Johnston, Beauregard, and Bragg is actually the one that we can see and have the ability to judge him by:
Albert Sidney Johnston had the trust, respect, and confidence of both President Davis and his subordinates. That is something that only 1 other Full General in the CS Army possesed, and that was Robert E. Lee.
Bragg had the confidence of Davis, but not his subordinates. Beauregard and J. E. Johnston had the confidence of the men and the public, but not Davis. Lee had everyone's confidence, and thus was much more able to effectively command his army.
I dare say that having a competent, trusted army commander in the West who was free to operate like Lee was in the East, that would have been a Godsend for the South.
Kirby Smith wasn't exactly setting the woods on fire in the Trans-Mississippi, but I think being fairly free of Davis' micro management & oversight worked to his advantage.