Nick, a suggestion for historical realism: you're talking about highlighting skirmishes with about 2,500 per side, which is roughly large brigade size at Gettysburg. Because of the spring's warfare a large number of brigades were commanded by colonels already and even more took charge during the battle. The Union's First Corps, for example, had 3 of its 7 brigade commanders on the morning of the first day at the grade of colonel, and 5 of 7 by the conclusion of the battle.
But more importantly than what name to put on the officers, I think it brings up something else awesome about your game. The computing power of modern technology means every game is designed with the false notion that the key to the battle is Major General George Meade or General Robert E. Lee. But in reality, Gettysburg was won as much by Colonel J. Lawrence Chamberlain and Lt. Col. Rufus Dawes at the regimental level. And reading their reports, it's evident that a whole host of unknown majors and captains and lieutenants made those decisions. With the limits of numbers leading to your decision to break up the battle into its individual tactical components, you're creating a product unlike any other--one that actually reflects the dynamic experience of warfare.
And if you successfully create a way where success or failure then affects all future battles (i.e., achievement of the objective is not required for continuing the game), well, you've really got something, sir. So consider really focusing on colonels, and those individual moments!