Union West: O M Mitchel and George Thomas on the West, for recognizing the value of Eastern Tennessee (and Chattanooga especially for the former).
Union East: Kearney, probably (though probably he'd be too impetuous). McClellan should have been retained as General-in-Chief of all US armies and kept out of the Army of the Potomac, instead of the other way around. He made good strategic plans but could not execute them.
Confederate West: Bragg should have had his rank raised in 1862, so that Kirby Smith (Van Dorn as well) was under the former's command during the Kentucky Campaign. A coordinated attack could have defeated Buell's force and retaken central Tennessee.
Confederate East: This will be controversial, but Lee. The Confederates needed to make their victories count for something. A good general-in-chief - someone who understood what the South needed to do strategically to win, including the prescient idea that Northern public opinion was important (hence Lee's Gettysburg campaign) - that was what the South needed most (it had plenty of good leaders, as shown). Both Bragg and Lee did some thought on this issue, but Lee obviously would have been the better choice.