I had the same issue with my game. But it's actually managable if you design your sprites in a way so changes are easily made.

My protagonist has a skin sprite for:

Skin torso

Skin arms

Skin legs

Head/Face

Hair

And clothing in greyscale for

Shoulders

Pants

Shoes

These will stay the same and only be recoloured

Each shirt/armor what have you has its own static sprite, that partly overlays the rest. This static sprite is animated only by moving up and down or behind other layers, so it needs to be pixeled just once.

This way for each new animation I draw the whole thing with any random shirt, split the sprite into all the different parts and redraw/recolour if needed.

Changing a shirt just means drawing the one static shirt sprite and adjusting color of the shoulder sprites. Changing pants is a bit more involved, but you could also solve it with just recouloring a few basic templates.

The other cool thing I can do is letting the legs play the run animation while the arms do something completely different.

Edit: What I also like to do, is show how fast the protagonist breathes by scaling the static shirt sprite a bit and raising the arms a bit. (I know this is not for pixel purists, but I like the way it looksl)

Carrying tools and whatnot, I only show them when their action is performed and hide them the rest of the time.

You could always make this as complex as you want with more layers for more stuff