Having a choice of skin color sounds nice, in theory.
Assuming it is told from a third person perspective, you're increasing the size of the game by more than 90% (based on the notion that MC is seen in most renders) for each additional skin tone. Couple that with requiring redone facial morphs as well, that's even more work for the art team. Take a look at existing black characters in VNs such as Dreams of Desire or Acting Lessons, and picture them with just a color change. They would look "off". Different races have different features that wouldn't quite look right with just a skin shade change. Nose, lips, eyelids (particularly important for Asian ethnicity)... regardless, it's not worth the hassle.
Beyond that, you run the risk of offending people if you start down that slippery slope of stereotypes. Black guys with huge dicks, Asian guys with small ones. Oftentimes, it's easier for art teams to work on what they're familiar with. I don't know how many devs are non-white/asian as most VNs tend to be in English (many times it looks like bad MTL of the native tongue), Russian, Chinese or Japanese.Three of those aren't predisposed to having black or Latino populations.
But yeah... getting the option to choose skin tone is a bit of a pipe dream.