Right, except you just chose every players' play style for them. If the player doesn't go high enough into magic to get your super-duper anti-SOD steam rolling spells than any competent AI will build SODs out the ying-yang and crush them. What does the civilization focused player do? What does the other military based player do when their SOD is on the other side of their empire? Magic is only one play style.
Let's add some buildings for the civ guy that gives high attrition damage to attackers (%-based to simulate starvation and diseases which the attacker has to deal with). Add a new category of super-combatants that do increasing damage the more enemies there are. Problem is, balancing those is much harder then adding some spells that are able to combat the worst of a stack of doom. (And also spells make more sense then some mobs that just happen to do more damage the more enemies there are. ^^ )
Also magic is fun. 
The right balance of subsystems not only makes SOD steam rolling a non issue, but can make the strategic/tactical interplay much deeper. The resulting game would be much better (this is all predicated on our not really knowing the full scope of what we're getting in EFE of course).
Yes, but most likely we won't have such a system in FE. We won't get a siege system (as said by Derek in some other thread), battles lasting longer then one turn won't go in (would need too much of a system change), etc.
But even then, take the Total War games. They have most of what you've just described. End game consists of a few (2-3) super armies conquering the entire map with ease. All the systems there won't slow you down once you got a critical mass of units (and the economy to support them).
The problem is that attacking in one place with massed forces against a spread out defense line always gives you victory if the enemy is not able to counterattack or reinforce their defenses in time. In games it is usually made worse by the attacker suffering almost no casualties when attacking with overwhelming numbers. My examples with the magic spells were to solve one half of the problem, by making sure the attacker suffers heavy casualties to reduces his numbers. Giving defenders time to reinforce won't go in as long as we won't get a siege system which, as has been decided, won't be in FE. (The other solution being teleports of course, which imo cheapens the whole strategic part of the game.) City militias with big defenders bonus could make super stacks even more necessary, to overcome the defenders bonus though. :/
Making counterattacks possible is simple, make the AI do it's own superstack and attack. But then you have blob combat, stacks of doom in a race who can conquer more faster.
Since there is no sort of terrain ownership or larger zones of control, encirclements are not possible (and would be a bit silly in a fantasy game). Also no supply lines to sever.
Limiting the numbers of units in a battle doesn't work too well either, since if your first attack loses, you just send another wave. The enemy will always have less units then you have.
As far as we know, we won't have a morale system, so it's always a battle to the death.
So yeah, I see not much possibilities to make the stack of doom attack not work with current system without a total rewrite. There are some (more or less) gimmicky solutions like spells to make superstacks vulnerable. But then, I'm not that imaginative anyway, so I wonder how it will be in FE in the end. 
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Personally I'd love a Morale/Organisation/Exhaustion system à la Hearts of Iron. You'd have morale on a per unit basis. Now any action you take depletes some of that and it replenishes each turn by a bit (but it takes a few turn to go to full again) low morale makes a unit weaker or even prevents it from fighting and moving. Morale increases faster in your own territory. Movement in enemy or barren territory, fighting, losing units in battle, taking damage, etc. would all lower morale. In a battle with a large versus a small army then, the small army could win by inflicting enough morale reducing status on the enemy. Be it using magic, killing the enemies front line troops (army wide morale penalty for every dead unit), etc. Attacking a city would cost the attacker a bit of morale each turn and so on. The defender has it easier since morale is higher in its own territory and it thus could act faster again after either a win or a loss compared to an enemy. So, perhaps the defender would lose most of its battles, but eventually they could inflict enough morale damage to the enemy that enough enemy units are unable to fight.
Or the enemy makes a forced march towards a city and captures it. Keeping that city under control while regaining lost morale from all the distance covered and the battle itself would force it to stay there for some time before it can work effectively again. And during that time it would be vulnerable to counterattacks.
But yeah, that's not very likely to get implemented anyway. ^^
Edit: As for the topic: When the AI is able to use superstacks too, I've got no problems with it in the game. Only when the AI refuses to use them and thus can easily be steamrolled it bothers me. So, go frog go, make the AI evil.