One of the problems with the previous games was the tendency for small skirmishing armies to simply be wiped out by neighbouring fullstacks. I feel that the way in which troops movement was simulated didn't allow smaller armies to be used effectively, and the game ended up being a fullstack fight. These are some of the things I think would allow smaller armies to be used more effectively.
1 - Make armies movement points reduced in proportion to their size (of course factoring in other things like terrain and supplies as well) - basically make size a factor. This would be for standard movement as well as flight and pursuit. This seems like a basic element of logistics.
2 - Allow certain types of units reduced penalties for harsh terrain (ranger/pathfinder/huntsman type units should be able to traverse forests and snowy environments better than a full army of cavalry/infantry/supply wagons)
3 - Use the area-of-control style interception that ETW and S2TW did (they probably will but I thought I would add this in as it is important for ambushes)
4 - Allow smaller armies to move unseen through most terrain unless detected by agents or other armies on the campaign map. Make certain units better at hiding and certain units better at detecting concealed units (This would take away some of the omniscience of the player on the campaign map and would make tactical movement of troops more an element.
5 - Alter the win/lose nature of battles. This would be tricky, but as a lover of skirmishers I don't know why I "lose" when I unload hundreds of javelins and arrows into a much larger army, then retreat away. I lose few men and they lose a big chunk of their forces from my harassment. Feels like I win in my mind.
6 - Allow units to remain concealed even while moving in the battlemap, assuming they are in appropriate terrain. Detection would be based on their skill as ambushers and the ability of the enemy to detect them.