Today I did something cool! One might argue that working on something of a purely cosmetic nature under game jam conditions is a waste of time, but in this case I feel it's time well-spent as it's something I'll be able to use again and again for any pixel art games I make in future (I don't foresee myself doing 3D so that will likely be all of them).
So what did I do? I made it possible to recolour parts of sprites using a pixel-shader, which I think will produce vastly superior results to the approach of copying the sprite and changing pixels on game load for every variant you want! I can't really take any credit though, I just spent the time fiddling to get it working in my game, the true genius here is someone who calls themselves Jinxology who was kind enough to post their code on the Unity forums - thank you!
It's a bit hard to see here due to the poor contrast, but I'm using a single sprite with the hair being recoloured based on the player colour:
Tomorrow I'll hopefully get around to making squads move - if I have enough time I might even get sidetracked into a very basic fog of war / stealth mechanic that hides enemy squads from you...