All creatures are affected by the size of the stack.The more creatures,the harder to coordinate their attacks.So,even though a larger stack means bigger damage,it also means more penalty on that damage.This penalty would usually be some -1 per weekly population in stack(calculated to the final damage,and not affected by any other bonuses/penalties).So,while larger(and usually stronger)monsters are doing more damage then smaller ones,they are also harder to coordinate and thus deal less damage when in big groups.That is,unless they are leaded by a skilled hero.For each level of the hero,this penalty is reduced by 2.Also,if a hero has a specialty in that creature,the penalty is reduced by 1 more per level.There would be exceptions to this,of course.
For example,units with formation(such as squires)would have a bonus instead of a penalty.
Loose troops,like archers,would receive neither bonus,nor penalty with the growth in their numbers.
Casters,however,would be synergetic and would sacrifise their initiative for aditional damage.With their growth they would receive -1% to their initiative(its harder to focus so many casters on the same target),but only after casting the magic.Their magic,however,would be more potent,and would receive a bonus to damage.Casters,however,arent affected by heroes level,but by his knowledge.Each point of knowledge negates 1% of the initiative penalty(but does nothing to the attack bonus).
And mind you that +/- to the total damage isnt anything special.Maybe percents would work better,or -1 for every 10 creatures,or something like that would work better.
And if you couple this proposal with this one,this one,and this one it would really be hell of a game
(hell of a game for developers to make,but also hell of a game to play 
)
Also,here Ill mention homeworld again,and say that it also has very complicating things in it(physics of the movement of the ships,physic of the beam weapons,physics of missles,etc),yet it is quite easy to learn.Its all just in the implementation.
