This would be awkward to try to explain in game, so the easiest way to implement it would be to stop having duplicate equipment slots in the first place. Weapons are easy: warriors get Weapon, Off-Hand, and Ranged; wizards get Staff and Wand; priests get Divine Weapon and Holy Symbol (either Holy Symbol gets 6 cards, or priests get another slot). The items get a bit trickier. Here's my first attempt: wizards get Orb, Pendant, Circlet, and Arcane Ring; priests get Charm, Talisman, and Divine Ring.
This would make the card/equipment crunch at low level much worse, I think, even if all of the types existed. There's no logical reason to restrict items in this way, certainly not per team. I would be mightily unhappy to have two or three copies of a Legendary Item in my inventory sitting unused, for example.
You're right, the low level items would need a lot of rearranging and rebalancing, and it may already be too late for a suggestion like this. Actually, that is my reason: allowing a char to equip 3 or 4 copies of a legendary item gives a large advantage to players who buy epic chests.
There's a whole other debate about gear from bought chests, but if you're only allowed to use one item per team, the incentive to buy chests drops, the amount of pizza bought drops, Blue Manchu get less cash to fund the game, it withers and dies.
