Could you elaborate on why Wharton?
Well, I was thinking of an East or West thing.
For the Eastern Theater I would want Stuart becauase, Gettysburg aside, he was devoted to his duties as ANV Cavalry Commander and was rarely if ever remiss in performing those duties.
The West, on the other hadn, was a bit more difficult. Naturally Forrest jumps out at you as the best but, as I said, I prefer him in a more indepent role than Army Cavalry Commander.
Morgan's a possibility but his decision to ride off into Kentucky, Indiana and Ohio was a mark against him for me, impulsiveness that lead to ruin.
Wheeler is useful in close quarters with the Army but less than effective further away from it. For performing all the tasks required of a Cavalry Commander attached to an Army Wheeler seems to fall short, not least for his habit of losing control of logistics and seeking fights.
Wharton appears to be an adventurous but more cautious commander than Wheeler or Morgan. He performed consistantly well and next to Forrest he was probably the best Cavalryman that Confederacy had between the Mississippi and the Appalachians, a bit too ambioutus perhaps - he had his faults and failures of course but so did everyone.
The fact that Wharton wasn't the showman many of his contemporary Cavalrymen were and that he was killed by a subordinate before the War was over - leaving little in the way of literary work behind - means that he's quite unknown.
More about Wharton here if your interested:
http://www.terrystexasrangers.org/biographies/submitted/wharton.html
And, just because I think it would highlight why I think Wharton would be a good Army Cavalry Commander, this is an extract from the closing points of that Article:
Galveston's Judge James Love writing during the Spring of 1863 observed that Morgan's and Forrest's commands were known for their many successes in independent actions. He went on, however, to state that Wharton's abilities were more important but less noticeable. Wharton's men could work successfully with the main army picketing the front between battles and during general engagements would hold the flanks. Robert Bunting some six months later made such similar observations that one suspects that Love and Bunting must have spoken among themselves on this matter or at least have discussed the matter with someone in common