Played a game of Command Decision awhile ago, and I came up with this idea. I think GM's, instead of leaving the players to choose a leader and develop their own strategy, should give each player a set of orders specific to their command.
Left to their own devices, players will listen to the strongest personality, whether or not he's the best and/or most experienced player. If you had your own, specific orders to carry out, there wouldn't be a need for an overall commander. Plus, it opens up the interesting possibility of having "winners" on both sides.