One can have a item stack with lore/enchantments/etc as the OUTPUT of a recipe, however one is unable to specify that a specific type of itemstack is required as an ingredient.    Adding the ability to pass an itemstack as an ingredient rather than just a material/materialdata would greatly increase the flexibility of the current recipe system.   

For example if you had a recipe that called for a diamond helmet with unbreaking and a iron helmet with unbreaking, it would craft a chain helmet with unbreaking,    whereas the non enchanted versions of these items would craft nothing.

This would also have the added bonus of showing the correct items in the recipe book, meaning that when known one could click on it and it would show the itemstack required (diamond helm with the enchantment) rather than just the raw material (diamond helm).