I've been thinking about having a semi-2D battlefield, with 3 fixed lines: center and left and right flanks.
The way to avoid the "everything in left flank" abuse is obvious: Players can pick a line, but whatever line has the most men in it automatically becomes the center. So if some army puts everything into the left flank, the left flank becomes the center, any stray units that were put into center or right flank would become right flank, and left flank would be automatically empty.
The real difficulty with this is not the setup, but the movement between the flanks. The closest I've come to a solution there is to only ever allow movement into the center, never out of it.