I think that's a perfectly good question for this thread. Our original OP said Lee should have been a regimental commander and that's it. Since Johnston was shot, who then should Davis have selected to fill the vacancy if not Lee?
Well, that leads to the question of who else would be in line or available.
G.W. Smith actually was Johnston's first replacement but suffered a nervous break down and was replaced by Lee, so that rules him out.
Beauregard going AWOL after Corinth removes the possibility of both him and Bragg, as Bragg replaced Beauregard in command of the Army of Mississippi.
The Lieutenant Generals appointed later that year were - as far as I know, in order of seniority - James Longsteet, Edmund Kirby Smith, Leonidas Polk, Theophilus H. Holmes, William J. Hardee, Thomas J. Jackson and John C. Pemberton.
Of these, at the time of Johnston's wounding;
- Longstreet is with the ANV and commands a Wing
- Kirby Smith commands an Army in East Tennessee
- Polk commands a Corps in the AOM
- Holmes arrives shortly after Seven Pines and commands a Division
- Hardee is with the AOM and commands a Corps
- Jackson in the Shenandoah Valley commanding, defacto, a small Army
- Pemberton is in South Carolina and Georgia commanding a Department.
Likely Jackson can be ruled out becuase of his on-going work in the Valley, and Polk and Hardee are unlikely to be transferred from the AOM due to the above mentioned change in commander.
Which leaves Kirby Smith, Longstreet, Holmes or Pemberton, with Longstreet the most likely.