I don't know enough about art/coloring/shading/etc. to really have an informed opinion on this one way or another.
I will say that after looking through the thread and seeing the examples of the art of Nessa, as well as other black Nintendo characters provided by DigitalOP there DOES appear to be a bit of a problem is regards to the lightening of their skin tone in fan art. I doubt any of it is intending to be racist, hell most of these artists probably didn't think about it at all, but unintentional racism is still racism, and I can't fault anybody who has a problem with it.
Whenever a white or Japanese character is portrayed by a racial minority in cosplay/fanart/etc. there's always a vocal population decrying "just make your own character." Then, when we actually DO start to get some dark skinned/black representation, people turn around and make em white/light skinned. Shit's stupid.