Only a chunk of my post was aimed at you. I admit, my posts don't tend to be very well organized so they might be confusing. Ill try and focus down a bit more.

This would be the main issue. Having to leave some guards to protect your crops, if they are near your borders is fine. I would expect my heartlands to be pretty secure though.  My issue though, would be that having unprotected areas get stomped would force you to leave too many troops at home. The system wouldn't be able to tell if your troops were attacking in small units or one super stack, all it would know is that they are elsewhere. And if the rate of barb attacks does increase with increasing proximity of your troops to each other, you might as well just hardcap the stack.

If an empire gets big enough, it would have so much area to protect that it would become unable to send enough troops to attack people, and if someone attacked it, the empire would not be able to defend itself. If it moves troops to stop the attackers, than the farms it is leaving unguarded get hit by barbs.

For that system, i get the feel that it either is effective, at which point it would seriously hamper all military action, not just super stacks, OR, so light enough that you can still send troops out to war, but that means super stacks are still in.

Most players would move the groups around separately, and then join all the small groups together right in front of their target, kind of an instant super stack. And the AOE spells, at least as i imagine them, won't totally destroy an entire stack. Sure summoning a volcano spell would vanish a whole stack, but i thinking most would be more like the AOE spells weakening the super stack so it can be easily defeated, not destroying it outright.

Given all that though, I think that while we want to decrease the prevalence of super stacks, i wouldn't want to get rid of them totally. In numerous situations they make the most sense. Attacking a capital? better have super stacks. Picking a fight with a dragon? bring a super stack. Even IRL, super stacks were how wars worked until after WWI when folks discovered that massing a million troops meant nothing to a chain gun on a hill.

Basically, my big worry is that we will put so many restrictions on super stacks that it harms all military stuff and makes invasions and the like impossible.

I remember I was posting in a thread maybe 6 months back when we came up with an interesting idea to remedy this issue.  Basically, each soldier would have a range around them that would include other armies in a battle if they were attacked.  In other words, soldiers in a radius of one another would be considered the same army, even if they weren't in the same tile, both for battle purposes as well as movement.  This would prevent people from making and remaking armies to zip around quickly. 

Also, if that isn't your cup of tea, you could simply incur or forfeit movement when combining armies, which would also would help resolve the exploit.

I hope magic isn't the only deterent to having only 1 huge army.  I think the best approach is to look at  scenarios where no magic is available.  I am sure with modding or maybe just game options people will turn off nuke type spells so I don't think it should be the only response.  Also there is the possibilty of counter spells (dispel magic or a global spell lock down type of spell) stopping them.  The main reason people use multiple armies in the real world is because there are many objectives and it takes time to move from place to place.  Having everything in one spot leaves you vunerable everywhere where that army isn't.  If the scale is set right than massing all your units in one place should be a sure way to lose if the opponent uses the right strategies.  World size might change this but on larger maps this should definitely be the case.

Something to note about Elemantals magic system and uberstacks, The volcano of doom spell frogboy mention presumbly requires essence. This in itself helps balance it out as taking out armies repeatably in this fashion will quickly reduce your magical strengh.

Call to Power had a simple answer for this:  Stack limits of 9.  

In that game, you would generally produce say 5 muskets and 4 cannons, and the cannons would be in the backrow until 2 muskets died and a cannon had to come forward.  

And of course you would have stacks of pure cavalry for maneuvering around your enemies as well as catching up to the tail end of your invasion force.  

I loved the system, far better than generic Civ ultimate stacks of doom.  

Usually in a war waves of 9 stack armies would roll across the world in long trains.  On a big enough world, I even had modern artillery arriving on ships before many of my musket stacks made it all the way to the enemy...  

Of course it would be different here, but I think limits have their place when it comes to stacks.

Stack limits stink and cause a flight toward quality.  Quantity should be valid as well.  Think Russia during WWII.

Well as some mentioned Age of Wonders in here, it would be great if Stardock implemented adjacent armies coming into fights. And depending on where they came they were located in that part of tactical combat.

However, AoW did have heroes that could by themselves take on entire armies. I had heroes in AoW1 that could simulatenously take on multiple dragons, cast an AoE spell and dodge the attacks of yetis, cheap fighters and strike back successfully like Drizzt Do'Urden. As the OP mentioned, I don't want offspring become super saiyans, though I want them to be decisive in battle than can take on entire single units.

It would certainly be an interesting battle. Especially if the 5 thousand peasants are led by a Champion with Command/Organization benefits, and imbued with the ability to cast "Quickened Blood" which doubles the attack speed of my peasants and increases their movement by 50%.

Either way it will most likely be a Pyrric Victory, at least if I were to win. I suppose theoretically, say if I was an AI, you could get away with little to no losses by setting ambushes and running away, ect.

a sufficiently poor AI might even allow you to take only half losses with fighting the entire army in one huge tactical battle.

I would certainly like to see peasant armies, if defeating armies better equipped, to be able to scavenge the weaponry and put it to some limited use. Definitely for the Champion, of course, unless he has some mystical weapon of what-not.

Of course, this is assuming lack of almost all magic (other than that via the champion) ... so with magic involved, it sets a new standard, although this argument was assuming and equal investment in melee if I heard correctly.

Why would adding a champion reduce the number of peasants to 2500? Having champions doesnt seem to require much of an investment (at least if its just the ONE champion) ... after all your Knights of death probably have a couple champions as well.

Still ... even without bonuses, the basic scenario of 5000 peasants equipped with leather gear and sticks vs 450 mithrilar knights simply raises a balance question of stats, without any actual stats involved.

I assume you mean that you are using some form of Refined Ore that gives a +1 or +2 bonus on the basic attack and defense values, as well as extra training that increases your HP by 50% or more. In addition to all the bonuses riding on a horse entails.

In the end, which army requires more investment of time, raw materials, and gold? Which army is more cost effective? Are they both cost effective?

Back to the question of Champions or no Champions, Either we can Assume the Champions and Sovereigns of both teams are off exploring, or that they are both present. I was assuming that your champions were "Stronger" while my Champion (or Champions) selected leadership traits that would increase the Viability of Mob tactics. After all, usually if going along the Elite path or the Mob path, one would tend to invest in skills and technology that synergize with their troop choice.

For instance, Your buffs would increase the strength and defense of your units (since your speed and morale is already high) while my buffs would increase Organization, Speed, and Morale (which are really all Organization).

As for the Heavy Charge Bonus, I should think the strength of the charge depends on relative terrain, flank, and wether you are in a block or a wedge formation. (If you are in a wedge formatoin the lead has a heavier charge, although more vulnerable to being cut-off and killed early ... or any arbitrary difference).

In addition, if Charges take place against a single cluster of units from three different directions, then the effectiveness of the charge is increased (at least in terms of Morale). However, the size of the charge in relation to the Victim-Cluster also relates to the effect of the charge.

If 5 Knights of Doom attack 200 peasants from 4 different directions, then the flanking will increase the charges' morale effect, however 5 attacking 10-20 defenders on the edge of the 200 man block is less effective from an Attack standpoint than say, all 20 Knights charging the same 20 defenders. Only practice and experience will teach you what is the most effective. Maybe the morale detriment is enough to split your force into 4 attack wings. ONLY if lead by a low-morale leader and low quality troops. Maybe a decent leader has enough morale to hold back your initial charge, which is less effective in damage than a 20 man one sided charge.

Maybe high morale Rabble are better to Charge at from one side with 20 units. Obvoiusly if each side of the block only consists of 10-20 men, then it would be more viable to attack all sides with 20 men than 1 side with 80 men.

Perhaps when facing 200 swordsmen of medium rank, its best for a 20 men elite Knight team to split into two groups of 10 and attack from the front and the rear.

Perhaps when facing 200 "Spear"men, it would be better to send 50 weak peasants to fight their front, while your elite knights encircle their flank, or attack other units. Sure the peasants won't last long, although knowing (from experience) how long they PROBABLY will last, and time running your spears into the flanks of the unit during the time you think your peasants will still be some-what alive. Then, hopefully retreat your Knights before the peasants all die, and charge the spearmen with another round of melee troops.

Lets assume that 200 of your Knights are bowmen, 150 are lances, and the other 100 are longswordsmen Knights

Then lets assume 3500 peasants use clubs, another 1000 use spears, and another 500 use polished Iron spears.

Sure, these are arbitrary numbers, although the actual numbers would depend on availability of the weapons, relative Cost effectivness, and over-all strategical and tactical decisions. Maybe its better to train one Elite Company of Fire-Iron pikemen, and the rest with flimsy clubs and sticks.

Or maybe its more effective to use 3500 bronze spears as opposed to 5000 mixed troops, or maybe 2000 Iron Spears instead.

Maybe its better for you to wield 200 elite troops with Magical +4 Steel Lances, and 4 well equipped champions, than 450 Iron-Clad death knights.

Maybe its better to have 100 Elite +4 troops and another 200 iron equipped Knights, along with 2 champions well equipped.

Maybe its better to have 20 Champions of varoius level, 5 of which are above level 20, and 1 of which can summon magical monsters and undead. As well as a guard of 100 average iron knights.