I recently decided to hop back into ts3, starting with only the base game. I installed default skin and eye texture replacements but when I go in game they only work if I edit pre-existing sims or create new sims.
While this can help, I have found that it doesn't always work properly, especially in the base game world of Sunset Valley and all the EP worlds (perhaps due to them having static caches in the game root folders?). Editing them in CAS then seems to be the only way, and even then chances are that they will keep the default skin for whatever outfit they wore when you started to play the world.
Another way can be to duplicate their outfits in MasterController and then deleting the original ones. The first part is done under Immediate>Copy clothing between categories and the second one under Basic>Remove Outfit. Always remove Outfit 1 and change them into Outfit 2 of the category they are currently wearing before you delete the first one in that category, too. Change them with MasterController, too: Basic>Outfit, otherwise the numbers will reverse. No guarantee though that it always works, but this is also a way to fix it when their thumbnails become wonky.