Don't get me wrong, the available options in X & Y were extremely limited and restricting, but that doesn't change the fact that character customization as a whole fits right into the Pokémon games. A key element of the games is that the silent protagonist acts as a self-insert--if the player chooses, they can imagine themselves as the protagonist. The ability to chose exactly how the protagonist looks adds to the immersion: you can make yourself look however you like. This is truly your journey, and the protagonist is how you want to present yourself. It was definitely a greatly-missed feature in ORAS, where the option to customize your Trainer would have worked splendidly alongside other features such as the upgraded Super Contests and Super Secret Bases. This is definitely a feature that should return and be expanded upon, giving more clothing, hair, etc. options with each new game.
(As a side note: I replayed X recently and completely surprised myself at just how eager I was to check each and every clothing store and make sure my character looked how I wanted before moving on. It's a really addicting feature as it is, and I can only imagine how much more fun it would get if each new release added on to it and made it more in-depth.)