Off the top of my head, I can contribute a few names:
Confederate:
William J. Hardee: Hardee was one of the most respected officers in the Old Army and wrote Hardee's Tactics at the behest of Jefferson Davis during Davis' tenure as Secretary of War. Hardee was fairly senior during the American Civil War, he was fairly senior-lieutenant general on October 10th, one day after Longstreet's. The only issue is that Hardee's record is rather mixed-he certainly had brilliant and competent moments like his assault of Rosecrans' right on the 1st day of Stones' River, his delaying action at Averasboro, and the desperate cavalry charge at Bentonville; however, that glosses over Hardee's less than finer moments, such as his very lackluster performance in the Atlanta Campaign, and his negligence during the Tullahoma Campaign (this nearly cost Bragg the Army of Tennessee). Erza Warner's Generals in Gray called him one of the best corps commanders in Confederate service, but it feels like a superficial description when you study his career in detail. Nevertheless, Hardee is one option available.
Union:
Charles F. Smith: A very interesting what-if; Charles F. Smith was considered to be the model soldier in the Old Army and constantly praised by high ranking Union generals (Grant, Sherman, Halleck and McClellan all praised him). The initial days of the American Civil War saw him responsible for organizing the defense of Washington D.C. for 13 days until Major General Robert Patterson arrived, C.F. Smith was then sent off to Fort Columbus as he had been originally assigned to. Although McClellan sought out to have Smith in his staff, Smith found himself sent to Paducah in order to take charge of the Department of Western Kentucky, which was later absorbed into Grant's command. Smith proved to be a strict but fair trainer of volunteers and Halleck considered his troops to be the most disciplined in the Western Theatre (though Smith took that as a sign of how badly disciplined the other volunteers were). In addition, he proved to be an excellent administrator and greatly understood the importance of staff (though Smith would deride the quality of most of the men acting as his staff). His combat performance was good as far as his short record in the ACW shows. He correctly identified the weakness of Fort Henry and led his division skillfully at Fort Donelson. The only issue with getting him into a high position was his supposed Southern sympathies (proven false) that the newspapers accused him of, he was also around Lee's age.