Some of the Civil War figures that have made it into the game as commanders go against historical simulation. I've got a laundry list, but one of the most irksome is William Quantrill.
I think his official rank as part of the partisan rangers was captain, and he didn't claim anything more lofty than colonel himself. I've read that he never commanded more than 400-500 men. Yet because of the current limits of the game engine, he can command a division of thousands. There is no inclusion in the game of one of his major opponents from the Union side, Thomas Ewing. Ewing commanded more men (at least the brigade level), and officially held the rank of general from early 1863 until the end of the war. Not that the Union needs more generals, but Ewing had as much impact as Quantrill and other generals represented in the game.
I would like to see Quantrill removed from the game as a commander. Replace him instead with a raider, partisan or cavalry unit flavored with his name as the commander, and one or more of the properties he has as a commander; no command points needed. I would like to see this done with other "generals" as well, such as John Mosby. I play as the CSA most often and even though these commanders are extremely useful in the game, I'd like to see them gone.
If you wanted to get really fancy, you could make all the partisan ranger units on the map, save Mosby's and McNeill's, become part of a neutral yet hostile-to-Union faction in late Feb '64 when the Partisan Ranger Act was repealed. ;D
If the game is going to include men who could have more likely moved up in responsibility from the brigade to division level and beyond, then commanders like William Barksdale (*sorely* absent) should be there. Instead, the Confederates are plagued with commanders like Floyd and McCown. If those weak sisters are represented, where is Gideon Pillow? Where are the other run-of-the-mill Confederates like Sam Maxey?