This is just a quick modification to Nobuyuki's remake of Nokola's Hue Shifter shader. It shifts the hue of your sprite, except it skips pixels with a hue lower than 0.125. This magically makes it useable on human characters. No more cyan skin!
Simply design your character sprites to have skin that is some shade of brown, red or tan, and avoid these hues in your character's clothing, and it should Just Work. Outfits created using Color Theory will maintain whatever color coordination (or lack thereof) they had when the sprite was authored, as long as you avoid red, brown and orange hues. The sprite in the example MFA uses a Split complimentary color scheme, and both high- and low-saturation colors so you can see how it performs in a variety of situations. (Ideally, you would avoid similar, slightly off, clashing colors like this. Be more fashionable than me, folks.)
Blood on a sprite, the red inside of a character's mouth, brown leather shoes, wood items or details, and most real-world hair colors are also ignored. You could edit the shader to increase the hue ceiling to about 0.166, if you wanted it to also ignore blonde hair, but I felt like allowing more color channels for clothing was probably the better trade-off, as this makes authoring a sprite with split complimentary colors theoretically possible. (Via yellow, purple and cyan.)
Tested under DirectX9. I'd like to add more features, such as saturation and value modulation for the skin, but I'm running up against the instruction limit. If I upgrade to 2.5+ DLC later on, I'll see if I can do better under DirectX11.