Yeah, I like the idea of the "alternative factor" option through a criminal guild or something like the Aspis Consortium. The campaign model could have a few different common factor types out there that do this kind of business and the party would need to decide who they want to do business with.
I completely agree with being against the "magic item shop". From a "big picture" stand point, I just can't get past the security the place would need. Essentially they would all need to be the hands of big companies with lots of resources in order to protect the merchandise. With adventurers floating all over the place, why would these stores not be robbed constantly?
Some other ideas...
1) Weird story, but I essentially created the campaign setting for our 4E game, and then promptly stopped running it and became a player when someone else took on the DM mantle. Something I added in before then was a periodic auction held in a major city, organized by the Fraternity of the Forged. I had an organization of warforged that managed to capture their own Creation Forge and bring it to the city. In order to produce more of their kind, they have to feed the machine residiuum(sp?). The organization sponsors all kinds of adventures in the region to get magic items gathered up for disenchanting to fuel the forge. In order to finance their operation, they keep the "cooler" items intact and sell them in the auction.
2) Use someone like the Arcane, Mercane, Witchwyrd (PF 14). They could be stand alone merchants that the PCs need to track down rumors about, or the inter-planar merchants could seek out the customers. Once the PCs reach a certain power level, they are contacted by an agent and connected to the Witchwyrd network and told how to make contact again should they wish to make a transaction.
3) Although somewhat cheesy, I was an enormous fan of Neverwinter Nights' Underdark expansion where the game at one point gives you a genie bottle, only when you use it the genie that shows up is a merchant, not a warrior. I think his merchandise changed occasionally, and he would buy stuff from you. Although it is a little DM-fiat, it is also easy and perfectly explainable...the genie knows who currently has his bottle and he wants their coin, so during his non-summoned "downtime" he can specifically roam the marketstalls of the outer planes for items suited to the players. He would also know how much money they seem to have on hand each time he gets summoned, so he could tailor the items to their power level. Not because he cares about giving them something too powerful, but because he doesn't think they could afford it. Throw in a limited usage factor (1/week, 1/month, 1/3 months, whatever), and you have a portable way of getting magic items into the game that the players would want and getting rid of stuff they don't.