In regards to player owned shops, I'd like to see it done as a multi-window shop offering multiple methods of interaction.
Window 1: List items to sell, up to say 30 items at a time for a price the player sets.
Window 2: List items to buy, how many of each item you want for prices you set, VERY useful for material purchases.
Window 3: Offer your crafting services, in a way where you set the price on your service, other people gather the materials and use your shop to craft the items for them, they pay for your service & get their items while you get the gold from the sale of your service and the experience from crafting whatever they had made.
This is pretty much how Ragnarok Online did it and it worked beautifully, players seeking to buy specific materials could set up shop next to spawns of that material around the world and encourage people to gather it for a bit of profit, or those wishing to sell say, a specific level of potion, could set up in that level of area and increase their odds of making a sale.
That said, player shops do generate some absolutely horrid lag in highly populated areas, people tend to complain about lag now...imagine 50+ people crowding the bank in EC 24/7 and that's just from the shops set up.
I'd personally prefer an auction house or both, however if we only get player shops, this is how I'd like to see it done.