Saw this in a dream probably due to the fact that I play this game way too much.
What if you could split a two-commander unit into two smaller units, with the secondary commander of the split unit becoming the primary commander of the second resulting unit, and neither resulting unit having a secondary commander until they reform or return to the city? How many times have I wished I could split off just the cavalry from my field unit to chase down an escapee? Or, two equidistant and equally viable targets are in range and I don't need every infantry man in my troop to handle one of them?
Why not split them up sometimes? It comes with it's own natural benefits and drawbacks, too, since obviously going too long without a secondary commander is not optimal, but could be situationally viable.
It'd be easy to program as well, and you can even put the standard arbitrary restrictions in place such as disabling the option if your march queue is full, or making the split and/or reformation take a short period of time, similar to gathering runes.
Think about it, this idea rocks, and you can have it for free.
