A new shop that creates "quest items". For example, the blacksmith requests the following items: Excellent Rapier Fine Brass Toupee 5x Gold Ingots In return for the Brass-Flecked Rapier, which could be some TBD upgraded version of the original rapier. Or, Tome Of The Martyr Orc Painting 2x Silvery Nuggets In return for the Canvas-Wrapped Tome of Absolution. Etc etc.
A popular suggestion. Most recently here. http://forums.cardhunter.com/threads/suggestion-crafting.3986/#post-39275 If you remove the upgrade part and just have change the skin however would be an interesting touch! Otherwise I'd suggest just allowing non-loot items to be crafted for balance reasons.
If not upgraded then a crafting system, or ability to transmogrify the item into a similar item. There just aren't enough items total right now, you find players use very specific sets of items with little diversity. Having a larger item choice creates a more diffuse playing field and a tougher challenge for everyone.