I'm sure some of these ideas have been said many times.
1.Fire ,which can spread with tree,grass,wind. can affecr morale.can kill people. this one existed in CMx1,but lost in CMx2.
2.melee attack
3.random map generate, I think the reason of this one lost in CMx2 is the AI PLAN can not random generate, because of the ai plan is more complex than CMx1
4.dynamic weather,
5.CQB system in the command UI.
perharps one(more) of these hope can be added in engine5.0