1. Strategic challenge of defeating the many with the few or even "taking whole" a Sun Tsu term that indicates achieving victory without loses for either you or your enemy.
2. A disconnect between the commander and the soldiers. I've yet to encounter a game where I feel a kinship with my soldiers or populace (though the original COH comes close).
3A. Climbing the ranks, military command is earned. A soldier leans to fight, learns to follow tactical commands, learns to give tactical commands as part of an operation learns to give operational objectives as part of an overall strategy and if they survive and are bright enough, can learn to build strategy from a combat or logistical perspective. Most RTS just jumps to that last step instead of showing players "why they command".
3B. Obviously player driven soldiers (obviously 3A would enable this across all perspectives of the hierarchy).
3C. In the area of resource management, I think much more focus should be put on the effects of resource extraction, sustainable practices and the long term issues.
3D. Effect on civilian populace.