AC's solution was dumb (everything EXPLODES!!!!)
No, AC had was area damage that makes sense.
The solution to stacks is area damage, you can stack but be vulnerable to being bombed so megastacks can be wiped, the real issue with megastacks was because damage was mostly on unit it mean it would roll and unless they dropped a nuke nothing could stop it, allow bombers to deal area damage and things start to change.
Its easy to make the system reach a point were megastacks became impractical by simply allow zone damage and make the AI create mix units stacks, if you want to make a one unit per hex then make the concept of "army" and allow each army be composed of different types of units (archer, swordsman, etc ...) so you dont end up with entirely redundant units because they were designed for esorting other units.