The problem would always be that some players would try to exploit this to pass equipment around an alliance. Especially players that are upgrading Skull Gear. I think it would also really diminish the value of the items in the pro shop too, since you would no doubt be able to buy them just for gold now.
I would like to see the ability to save Perks from equipment, and store those perks in Runes to be able to implant onto new equipment. It would really make customizing your equipment easier, and give players the ability to try more strategies with what perks they use. Saving Perks from equipment would happen randomly when you melt down equipment.
Then lets combine that idea with having a marketplace, it would be cool if you could also sell these Perks for either Gold, Pearls, Gems or even Vouchers. Maybe let the Seller set the price that they want. So if I have a Skull Perk that you can implement onto your equipment, I can put it on the Marketplace for 500 Gems, or if I am hurting for Pearls maybe I would ask for 5000 Pearls. What would someone pay for being able to add that to their equipment without having to go through the hassle removing perks/forging and hoping to get it at 50 gems a shot.
Lastly to make this addition to the game beneficial to Flare, to place a rune in the marketplace for sale should cost Gems. I think 50 Gems would be a starting point, since that is the amount needed to remove a perk from your equipment.