Note that brigades are being stacked on the map, not on the player reference cards. I think the game plays more smoothly that way.
Long experience suggests that it doesn't play more smoothly that way. A faster and less cluttered game can be achieved by using the cards. I can punch out a three hour game with ease that way. We rejected cluttery stacks very early in the design.
But providing you adopt a sensible method for recording subordination you can operate a stacking system succesfully if you find this suits your style or preferred ergonomic methods.
This topic seems to have reached obsession stage with some gamers. There is a discussion on Consimworld about it with the leader of the "waste of time" brigade, Andy Daglish. Warning: not safe for children.