I don't know what plans staff had for this down the road. Maybe those plans or ideas change everything and make my opinion on this matter moot. Even if there are no grand plans I am sure that, with enough dev work, the skintone system could be expanded to address all the above concerns to a large degree.
Assuming there isn't a grand plan I am unaware of, I don't know if it's worth it though. I wonder if the easiest and best solution is to just remove skintones. Let layers define this in their descriptions/nakeds as they had all those many years before skinones were added to the game.
Heck, for bonus points, add a way for players to color text in descriptions/nakeds. Get that color eye candy some players love plus more freedom and creativity for their RP and character design.
Just a thought!