I was thinking about crafting some more, the system I had come up with, the integration with designed units, and what would have to happen to make crafting worth it rather than just something to min/max your champion.
In my proposed system the foundation for crafting were the elemental shards. The more you had, the more items you could make and the kind of shards you controlled determined what kind of enchantments you could forge into an item. That would still be there, but I would add in a few other changes to give a complete overhaul.
Blow up the whole magic tree. Take every tech related to magic items and change them. Instead there are techs that allow you to make general kinds of weapons, varying in strength. The categories could be (names changed in-game for flavor), lesser accessories, greater accessories, lesser magic weapons, greater magic weapons, lesser magic armor, and greater magic armor. What determines whether you can choose to make a magic longsword or just a dagger depends on your research in the Warfare tree.
When you unlock a tier of weapon/armor in that tree, it opens up that base item choice in the item creation window. There could be a few weapons/armors/charms sprinkled already sprinkled in there to give the AI items to use, but the concept of magic items is similar to the way units are created. When you craft a magic item, you aren't really making an item. You are making a prototype that you can then decide to use on your trained units or equip on your champions. The stronger items take more crystal and production cost or gold cost for champions.
Under the current system you could create a Boreal Blade for your units or buy one for champion just by researching the Arcane Weapons tech. In this proposed system you would have to research both War Colleges (from Warfare) and the Greater Magic Weapon tech (from Magic). You would also have to capture a few water shards or have the equivalent water power through buildings like a Hedigah Bathhouse.
I know the game could be perfectly fine and playable without any crafting system at all, and I would also rather there not be one if it meant sacrificing other features or screwing up balance, but I do see it as an option if done well.