A JSON/NBT based shader config system would improve the shader customization.
Adds:
-lists (Example: Selecting modified ores to be emissive)
-Compounds (Example: Customizing Block Light Strenght, color, etc.)
-String (Example: Selecting an item which enables debug mode)
Downsides:
-More difficult config sharing
This would be optional and only used when the shaderpack asks to