I think with the unique crafting recipes. You will be able to make weapons more powerful than you could through general enchanting. But, this naturally balances itself out since enchanting has the flexibility of putting almost any enchantment on almost any item where as magic weapon crafting requires specific recipe and ingredients and creates a specific result.
My opinion, not that it matters, soul gem for soul trap, void salts for electric weapons.
Yeah... those are good examples. But I was hoping for some specific recipes from you guys.

Also, while we're on the subject of uniques, their enchantments should really be a little bit stronger than anything you can craft yourself imo, especially daedric artifacts.
Yeah. Right now they're using generic enchantments but when I get the balance portion of things they will be given special enchantments.