Davis did want Hardee to take command, so he could prevent Johnston or Beauregard (his only two real options, whom he both despised for reasons both personal and practical). But Hardee flat out asked to be put back in Corps command, and he didn't want to command the AoT. And so, Davis puts Johnston in command. Johnston turns around morale in the army and helps with resupplying units with uniforms and weapons and such. Of course, Johnston was an awful field commander, being good at setting up solid defensive lines, only for Sherman to turn position after position, and had pretty much no real strategy. Johnston gets replaced by Hood, not by Hardee, because Hardee was as milktoast and rigid minded as it got.
Pemberton was an OK general. I'd say he'd have done better under better leadership; maybe he would have been better as an artillery commander. But his reputation is destroyed at Vicksburg, and his northern birth couples to make him very unpopular with the soldiers; hence why he doesn't get a corps command, but resigns, reverts to Lt. Colonel and commands artillery around Richmond.