Purchases are only in set locations or triggered by special events. Each purchase event should be handled differently. This can be achieved by something as simple as shuffling the item deck and only dealing out a few cards for each store visit.
When a player is doing a purchase price can be adjusted to reflect the plot. In friendly areas, prices are cheaper, and in unfriendly lands, prices are greater. If the game is led by a game master special items the player will need to complete the main plot can be slipped into the deck to help the plot advance.
Merchants are also a good place to give the players some key information or gossip.