This offers some possibilities for reflecting commander quality. The obvious one is to increase the bonus they give, but given the D6 nature of the Portable Wargame this is probably a bit extreme. There's no real way of reducing the bonus of a poor commander (make it zero and the commander has no purpose) and a +2 on firing, close combat and rallying is rather excessive. Another possibility is to vary the command radius, but increasing it for good commanders means that they are less likely to put themselves in danger - one of the side effects of the commanders 'adjacent' effect on a square grid is that they are best deployed in the front line so they can influence the unit they are with and those to both sides, but at the risk of being shot.
However if we consider that the commander is a point of focus of the army's activities, then it's easy to see one way of reflecting superior and inferior commanders - the ability to rapidly shift that focus and wrong-foot their opponent. This could be done by varying how far a commander can move - an average commander moves 2 squares, but a poor commander could be given only a 1 square move, whilst a good one gets a 3 square move. In that way a good commander can suddenly shift his influence from one side of the field to the other, whilst a poor commander will tend to be stuck with whatever plan they started with.
Another possibility is, of course, the initiative roll, which determines who acts first after the common artillery fire phase. There's a slight advantage to going first (you get to recover from, or exploit, the effects of the artillery fire before your opponent), so a simple reflection of commander quality would be to give a force with a good commander a +1 and a force with a poor one a -1.
I have also been considering how to reflect some of the desperate, and sometimes successful, charges of the Civil War. To this end I have considered the possibility of giving both sides a number of points of Elan - maybe one for each unit the force starts the battle with, maybe less. Whatever, it should be a finite resource. When a unit initiates a close combat it may spend a point of Elan to add one to the die roll (although do this before the defender rolls to add an element of risk, of course). In addition a defending unit may opt to spend two points of Elan to add one to their roll, simulating a desperate defence. The relative costs should slightly favour, and encourage, the kind of aggressive attacks the war seemed to produce.
This game is starting to acquire a life of its own, and I feel I really need to write it up properly and give it a name. Unfortunately all the best names for American Civil War rules have been gobbled up. I shall have to give it some thought ...