That must still be a pain in the less honourable parts to deal with.
I usually keep my infantry and militia in 3s or 6s depending on how many I have, but depending on what division names I get this can vary, especially with militias. As Germany for example my first 10 militia are all Luftwaffen Feld Division and they get split into two stacks of 5 (which are usually the main defenders in France once it's down). Garrisons are typically 1s and 2s, and I mix my mobile stuff together to get combined arms corps. I add the '39 and above HQs to them as well; alternatively I will have a powerful general lead a stack of 2-5 cavalry with an HQ.
Late game, sometimes I combine all the mobile unit types into six-stacks, but that's just for flavour. Even as Germany, I don't usually splurge two whole Panzer divisions on a single Pz leader. Even Rommel, Guderian, Manstein.
Commandos are in 1s and 2s, sometimes 3s, because they're always few.