Because it could be seen as white washing. There is no way to tell for sure why they did it, and no way they would admit to white washing if it did happen. We do know that companies, usually the bigger, are not all that progressive when it comes tom female protagonists, and non white protagonists. Shantae would fall under BOTH categories. On top of this, it's worth noting that Arabic people (or anyone with brown skin) are still not that high on America's 'like' list in the wake of 9/11. Taking that into account for Shantae, this is three strikes.
It is very possible that she was changed in the 'best interest' of the Kickstarter's success. Not that I am saying that is what happened, or claiming that WayForward is racist, or whatever. We simply don't know, but the possibility cannot be ignored.
Personally, I find it hard to believe that it was simply an art decision. Shantae's skin color is one of her stand out features, and a nod to the whole Arabian theme. If that were to be removed, it would be essentially a crime to the character and vision of the game in itself. I honestly cannot see any artist having the balls to strip away that from Shantae. It just doesn't seem reasonable, and furthermore it doesn't seem as though the art suffers at all from a tan skinned hero.
But alas, we will never know for sure. Certainly this also doesn't mean we shouldn't support the project. They did, after all, rectify this mistake.