While I can’t tell you for certain what you should change
without seeing both the sketch and the linework, I can say that generally this
is an indication that you need to refine your sketch more.
Go in and erase the ragged lines, structure lines and stragglers,
and overall thin out the lines you want to keep a little bit until they’re closer to the thickness you want for your actual lineart.
You’ll find that those
thicker, messier lines can hide a lot of flaws that weren’t apparent until you
started trying to do clean lines over them. A lot of artists prefer sketch work for that very reason.
Otherwise yes, you can try to keep your sketch and line pens closer in settings. I use the same pen for both and just vary the size a little bit.
Regardless though, getting the linework to look as appealing as the sketch is always going to be a struggle. And honestly it’s kind of a losing battle.
The smooth curves of Riley’s belly and mons pubis are much easier to make out in the sketch because I can literally draw in grid lines and thatch lines to convey that. I can’t do that with lineart. (Her face is also cuter because I couldn’t recapture it in the lineart with the time I had. It happens.)
It’s much easier to convey shapes, gestures, and depth with a sketch because it’s a looser style and leaves more to the imagination than clean linework.
Try to remember that clean lines aren’t really meant to stand on their own like a sketch is.
They act as structure for and work in tandem with coloring and shading to form a finished product and establish depth and shape.
EDIT: It also kinda depends on your style of lineart