I would like to see a more dynamic battlefield that simulates the push/retreat mechanisms of a real tactical battlefield. Right now it's simply about killing stationary targets, and the casuality rates have, to put it bluntly, nothing to do with reality.
To achieve that, you would need a better strategical AI. A good start would be to allow AI groups to retreat along the same path they are scripted to advance. You could set a certain threshold for how much incoming fire/casualties/morale drop the group could take before halting and then another threshold for retreating. The group would then retreat back to the previous waypoint and face the current waypoint.
When that is in place, weapon accuracy and effectiveness could be reduced to more realistic values. The game would then require a greater deal of maneuvering - not just frantic placing of target orders. You could have realistic probing missions and allow the scenario designer to script delaying actions.
I think the expanded victory conditions/objectives which were added in CMx2 have great potential, but they are rarely used. The game is usually just about killing/racing to capture the flag, like CMx1.