I've seen some artists fill in the flat-colours and then recolour the outlines to fit the nearest colours, have you considered this? :o

edit: albeit they're always a shade darker for visual reasons

agreed, making similar colors, maybe a darker version of the color it's against (let's say you added a certain # of darkness each time) and see how that goes, or maybe pick more of a grey as black may just be too high contrast

O.o I honestly have never tried this. So I'm guessing they keep their original sketch lines up until the very end, then outline with a color that suits the color of the area they are working with?

I take it this is digital yes? If so, one would keep the sketchlines or in completion-art take the inked lines, and go over them again (in sai I use Preserve Opacity) to fill in with a slightly darker shade of the nearest colour, making the lines less harsh.

It might not be a favored way, and maybe other people have a better suggestion. But you gotta experiment to find what suits you best, right? Maybe seeing it will give you some ideas :> Save often and play with your art!

What I do is ink with black(cause it's easy for me to track)

and then make a clipped layer on top of the lines only, and use dark colors, or just use a light color and then adjust it so it's not TOO light.

It's a lot quicker than actually picking out colors to draw certain lines. This is one reason I LOVE layers.
you can take major advantage of this :D

Thank you so much ;//; I am definitely going to try this with my future pieces. I've been toying around with my sona's design a little (nothing too major) and have noticed that the lines stand out too much in comparison to my colors. xD Also, coming up with eye colors that go well with the pink and white of my sona is difficult but I'll get there xD...eventually