I like the concept of having a limited, randomized set of magic items in a city but in my experience this just leads to players rolling for the items they want and banking their gold if they don't find anything they really want. Has anyone tried discounting the available magic items? I think that would encourage players to make "suboptimal" purchasing decisions without breaking wbl or player wealth but I'm not sure on a percentage.
It all depends on how detailed you want a shopping expedition to be. If your players like roaming the city, encountering cityfolk and finding various magic shops, it can work well. It can easily take up half or more of a gaming session, though, and if you don't have any intrigue going on in the city, it can feel like a waste of time for characters.
I like to pre-generate magic shop inventories, using a random generator like http://donjon.bin.sh/pathfinder/magic/shop.html.
Sometimes I'll modify results a bit, like add in items I like from 3 or 4 runs of the program, and I'll often declare certain items "always available", depending on the size of the city. Players can also "special order" things, but I find that rarely happens.
However, the bigger the city, the larger the number of locations where magic can be bought, and the more tedious it becomes to deal with it. I can understand folks who just say everything is always available, or give a percentage chance up to a certain limit.
Have you considered using Automatic Bonus Progression?
It gets rid of the big six (magic weapons, magic armor, physical/mental ability enhancing belt/headband, amulet of NA, and cloak of resistance, and ring of protection) in exchange for halving wealth by level.
I find if you remove those items, players have a lot less ideas of "saving up" for stuff and you can entice them to purchase things they might not otherwise do so.
It also helps if the items are interesting (but not necessarily mechanically powerful) but also not too expensive.
I'm using Automatic Bonus Progression in a test game and I like it, but I run pre-writtens and those can require some more work to keep the loot and wealth balanced. I do like it though and would love to try it out with a full party of experienced players (My games tend to start out with at least half new to Pathfinder).