It would be nice to see the API fleshed out a bit. Here's my wishlist:

• Ability to override item comparison for certain item. Useful if a mod uses NBT Data (since NBT Data isn't taken into account for sorting)
• Ability to provide a custom list of slots. This seems a lot better than expecting mods to follow a specific ordering schema.

The second one already exists: https://github.com/Kobata/inventory-tweaks/blob/develop/src/main/java/invtweaks/api/container/ContainerSectionCallback.java