I think one way to limit the huge advantage of large armies is to limit the width of the battlefield, based on region type. cities and rurals would be unaffected. Mountains--with narrow passes--would have a choke point 40 men across. Badlands, with their narrow canyons, would allow 60 men. Woodlands would allow 80 men. (undecided on towns).
I'm uncertain on the exact implementation. Woodlands would perhaps have a meadow, and so the length would be pretty even. Badlands could be narrower on one end of the battlefield than the other, like the end of a box canyon. Mountains would have a small choke-point in the center line and first defenders line, and get gradually wider on the other lines.
This idea, simple as it is, could add a whole new element to battles and regions and strategy.
