Clearly drawing on paper is still your greatest strength (though don't give up digital art, drawing on paper and drawing on a tablet will feel exactly the same after a while, trust this Internet stranger!). However, I think it would help a ton if you used the Curves adjustment tool in Photoshop, Gimp or Krita to make the pencil lines darker and easier to see, or draw over the pencil lines with a bold, black pen (though some color-correction in a photo editor may still be necessary).
EDIT: Wow, Clip Studio Paint must have some excellent brushes that emulate pencils perfectly! I guess just be patient and try to master one single aspect of the drawing process at a time, this stuff takes years of practice and helpful critiques before you can even call yourself a semi-pro.