Does anyone ever take the role of the generals in command and react the same way that they would? For example, if McClellan is in command of your army, after any large costly battle, victory or defeat, you retreat. McClellan will only be successful if you can avoid large casualties (on your side). One of McClellan's biggest faults was retreating even in face of victory (Peninsula Campaign, Antietam's lack of followup), but because of large casualties.
Playing Lee would mean that after any defensive victory you begin an offensive campaign regardless on the strategic situation (i.e., winning during the Peninsula Campaign led to Antietam, winning at Fredricksburg and Chancellorsville ended up in the Gettysburg campaign). With Hood in command, he attacks even when outnumbered and outpositioned. Etc.
This way, you play according to how your generals would behave in a situation. You get the benefits of Lee, but also have to deal with his over aggressiveness (i.e., you cannot just sit in Virginia and let the Union bash into your perfect defense). With McClellan in command, you have to win by 'out manoevering and out positioning' your opponent, avoiding a large battle and hoping to seige Richmond into submission. Any large battle with substantial Union casualties means that you must retreat back to Washington.