Still, I hope than XIII had color edit, one problem with ngbc is that if you change one color, you can totally screw the sprite, but it seems than in XIII there is a big use of colors, at least that's what I saw with all the color edits that SNK did
That was sometimes an issue in CvS2. Certain colors were pretty much unchangeable since they screwed up the character's outline, or other unrelated areas. With the new KoF sprites, though, I think the colors are designed specifically for easy palette swaps. There was even an article a long time ago about how they can change a character's entire outfit simply by swapping palettes, which used Yuri's leggings as an example. Raiden's bare chest would be another.
All things considered, a simple interface like CvS2's shouldn't be too difficult, I'd reckon. As long as your custom palettes display on the other guy's screen, or else that kinda takes the fun out of it.