I run a vanilla, by the RAW, game and it works okay. Here's a couple of ways to deal with Magic-mart.
1) get rid of the concept that you can get anything from one merchant. Maybe one city, but that's about it. Casters can only make the items they have the spells/levels/materials/feats for. Only epic-type characters can make anything.
2) Forget the idea of a crafter who has a "stock room." Making magic items takes XP and a large cash investment. Nobody burns XP without a reason even if they had the cash. So only items that are really useful (potions of heal, neutralize poison, scroll of identify, etc) will be "in stock."
3) Item crafting takes time, and lots of it. A +5 vorpal sword takes almost 7 months to craft and you have to work on it constantly. Not something you do lightly.
4) Realize that an item crafter makes a fairly hefty profit on each item and can afford to be picky about who they sell their XP, errr, wares to. Elves may not sell to orcs and vice versa. Being a hero is a good way to convince people to sell to you.
5) If the item isn't custom, the item already exists and the current owner may not be attached to it. Maybe you can track them down.
6) No one person, or even government, has the cash and resources to buy up every magic item that comes along, even at 50% value.
So the answer is to have numerous craftsmen who have a couple of the most useful items on hand and that can be convinced to make something just for you. People in a hurry can put out feelers (*cough* Gather Information *cough) and see if anyone is out to sell such a thing. I generally roll up several random encounters worth of loot. Okay, I use a program for it. My simple rule is to find the highest level NPC in the city and roll for the level and every lower. (So a 4th level paladin as the highest NPC means generating an ECL 4 treasure, ECL 3 treasure, ECL2 treasure, etc.) Not perfect but it gets idea.
Maybe the seller is using an agent, who gets a commission, to help sell the item. If you want a vanilla game, could be the agent fee + taxes comes out to ~50% the item cost. (Hey, real estate agents take ~10% as their cut. And magic items are, by comparison, more costly than 99% of the real estate out there) In this case there's no "Magic-Mart" but there is "Magic Mark", the guy who knows all the crafters, the adventurers with stuff to sell, and the adventurers out to buy.
I'm a big fan of auctions, I started using them in my game many years ago.