1.) Add more music options. Here's whats in my brain:
Custom (and the ability to make more customs)
Obviously these can share the same song by default, but it would open up customization much like the custom pixelmon textures do.
2 ) For fighting NPCs, in the npc customization menu, you should be able to pick which type of music you want. The custom music option would be perfect here.
3) the music box in poke centers should have an option to pick a music option rather than only play pokecenter music. This would be great for pokemarts and would be great for custom structures and people making custom maps.