I think there should be total customisation. Skin colour, hair colour, eye colour - the whole deal. Remember, you're supposed to be the player character, that's why they're silent after all. Just like how you can generate your own team. And when talking about canon and design, that's purely for canon only. The same way that Red has a canon team, though in the Kanto based games you can have whatever team you want, design is purely for consistency - you should be able to play looking however you want.
That aside, what I'd love is unlockable (or gained) equipment. Like something you get for defeating a gym leader, or the league. Maybe, if they continue the medals, you could even pin your favourite medal on your clothes. Combine this and full-body customisation, and I'm a happy bunny. (I'm dark-skinned, so I prefer being able to match skin tones as well.)