Animation. For one sprite you can have multiple different animations, each of which are played when certain conditions are met.
So, when your character is moving, you can animate the skirt's frills flapping in direction opposite to the movement. That is easy - just draw the frills on left side of the sprite.
If you have different animations for body etc., just split the sprite up into components - skirt, torso, hands, head etc. so you can control each sprite's animation without having to create dozens of complex animations for each situation.
Bonus points: when your character stops, animate the skirt suddenly moving to the front, then settling down.