I wonder, how difficult would it be to allow at the end of stacks movement to specify their formation? You could even tie it in to something I've been wanting to see in Civ for a LONG time. Strategic Redeployment. If the stack is making use of Road Movement, that stack must be travelling in a Column formation. You should choose your movement formation at the beginning of a turn, because it wouldn't be fair for a unit to be able to move in column and then come out into line for the next guys turn. Using Column formation you can remove the Commando promotion, you should be able to use anyone's roads in a Column formation, just expect to be slaughtered by any enemies along the way. At the end of the turn, if the stack is not in Column, you could have the player designate a defensive combat formation. Then on the next player's turn, the attacking force sees what's there, but doesn't know what formation it's in, until he commits the units for the attack. After the commitment, he sees what formation the defenders are in and chooses his attack formation. This could make spies a little more useful as well, they could be...attached to the formation and could report what formation they are using before the attacker commits.
Just a few thoughts, take em if you want.