Nintendo is already at the point where that is a possibility on the handheld's hardware since Monster Hunter Ultimate allows you to both customize the character and change your armor in 5 categories. We just need Pokemon to make that jump. The 3D models in the new game means that they definitely can implement this in the next series of games, if not sooner.
Also, I want the option of wearing a kilt for men. Nothing more badass than an Irish/Scottish Pokemon Master.