This is just my suggestion, I don't know if it's feasible: but it's based on these assumptions/opinions
1) The old system of champ stacks of doom was imbalanced
2) The current system is unfun
3) The real issue isn't champ stacks vs monsters, but champ stacks vs units as a rush tactic
My solution: In a single melee strike, a champion cannot defeat more then 1 unit in a group of units, be it monster or human.
Certain abilities would allow for defeat of multiple units:
Double Strike is two attacks
Sweep would hit 1 unit per tile
Magic
At the very least, what this system would do is ensure that building regular units would slow down or hurt heroes, as a group of 5 would pretty much be guaranteed to get at least 2 attacks in.