Neither region nor skin tone would be a good way to sort the images. To use examples of real players, both Antoine Griezmann and Paul Pogba have the same region of birth assigned, whereas in game Griezmann has the same skin tone assigned as Shinji Kagawa, David Silva and Henrikh Mkhitaryan; all these players are from different ethnic backgrounds and all look very different. The ethnicity variable isn't great as you said (another example is how the East Asian category bundles in China, Japan and Korea together), but unfortunately it's still by far the best variable the game provides to categorise everything.

I know that you can't view a player's assigned ethnicity in game, but every player in the database as far as I know has one assigned that you can view in the official Editor. I've always assumed this would also be the case for any newgen/regen generated, but I've never known for sure as you can't check this in game. If it isn't the case that regens have an assigned ethnicity then some sort of system that assigns images based on both region *and* skin tone would probably be necessary, although I imagine that would be a nightmare to get right.