My players for the most part don't have the Magic Super-walmart perception. The Only Shop they know of (and they have hit all the major cities just about) that sells Magic items is the Mages university shop. It has like a cabinet of potions maybe 3 rings a staff or two and a small case of wands say 10-12. They know the chances of finding anything but themost common item waiting on the shelf is slim. What the shop does is maintain who has what to sell on a personal basis and more or less brokers the deal taking a cut for the school. If the players ever bothered to find out the shop barely makes any money since inventory is pricey and some things sit for a while before being sold. They also operate as the place to commission I tems toi be made. the few mages who are artificers work through the shop to get jobs. The Shop takes its cut once again for being middle man. This to me has a few advantages, one is it seems to make a sort of sense that in a magical society a business like this would pop up and the university seems to be the best suited to handle it, second it keeps things centralized in one place so I as Gm can control the flow magic items and money, third it also keeps me from having to role play out every purchase with different people. Now when they shop they all deal with the one shop keeper and I usually play out the bargaining for the item. Very seldom if ever has a player gotten something at book price. They have gotten it cheaper or more expensive depending on a lot of other factors some arbitrary some not.
Now this is not to say that other cities don't have magic item retail of some type its just not obvious. The elven bard has no real trouble finding things sometimes in the elven kingdom. He has taken the time to curry favor and connections in the game and therefore can aquire items. Heck even once the dwarf while stuck in the elvish kingdom ended up teaching the elves in the church dedicated to the god of conflict great axe skills. And since he helped them out with out expectation of compensastion the elves offered to upgrade his armors enchantment for a small fee. Most of these interactions and such are how players, in my game, get items they want.
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