Well, the two biggest possibilities is that:1)Rainbow takes after one of her grandparents. Windy could have a parent who was darker, but either took after the lighter one, is a mix of the two, or had a lighter grandparent of her own. The gene for the darker skin would still be there, however, and happened to get passed on to Rainbow Dash.2)It could also be because of Rainbow's lifestyle. She is a very outdoorsy and athletic person, spending a lot of time in the sun (unless this version strayed from that greatly). While it may not be as noticeable as with white people, darker skin colors can tan as well. So if Windy spends most of her time indoors while Rainbow Dash is almost always outside, it could lead to the difference in shading.