Large army sizes have been one of those game design areas where we've never been able to find rules that please everyone. On one end of the spectrum, there are people who don't want any battles that are more than 10% larger than the largest battle of the era; for the Civil War that's about 200,000 total troops, or about 100,000 per side. On the other end of the spectrum, there are players who hate having any limitations on the number of troops they can effectively bring to a battle. For Crown of Glory we had much more restrictive battle limits than we do for FOF, in a mountainous region like Switzerland players could only bring about 40,000 men to a battle; I think we had about just as many players who wanted even tighter restrictions as we had players who wanted no restrictions at all.
Personally I tend to agree more with players who want tighter restrictions -- it just wasn't logistically possible to bring almost 400,000 men to one battle, and even marching with 100,000 men was often stretching logistics capabilities to the limit, and I think it makes the game more interesting when there are diminishing returns to the efficiency of attacking with large stacks. Perhaps the best thing to do would be to add game options to allow players to customize this, and to add better in-game messages explaining the current battle limits that exist in the game.