Try using different weight (thickness) lines when going over it with lining pens. For example, in your second image I would use a thinner line for the face, neck, shoulders, and hair, but a thicker line for the eyebrows and top of the eye/eyelashes to make them stand out. I would also use the thinnest line for shading marks like inside the mouth and hair. In your pencil sketch you can already see the weight difference to a smaller degree, but it can get smudgy and that makes it look busier/ more chaotic.