Here's some (late) input from someone that does large builds and therefore uses the shop often...
As a builder, I'm not fond (i.e. I hate the idea) of player ran shops unless there is a standard shop like we have now in addition to it. (And don't even get me started on the barter idea...) I have several reasons for disliking this idea:
1.) I don't see most, if any, shops carrying the volume of supplies needed for a large build. My recent fire genie build is a good example - I bought over 6.5k of web to make the smoke. I buy dirt like crazy, often filling my player inventory several times a day when I'm working on a big project. I can't see anyone selling huge volumes of common blocks like dirt and cobble because it wouldn't be very profitable, nor large volumes of the uncommon blocks because it would be more difficult to collect. We'll end up with a lot of little shops selling small amounts of items and builders like me will have to waste lots of time "shopping" instead of building.
2.) In general, players get very excited about an idea, jump all over it and then lose interest after a few weeks. I don't see this idea working long term except for a very few dedicated players like dph. That makes supplies unpredictable in the long term.
3.) When I'm planning a build, part of what I do is consider what's available in the shop if I run out of something. If we go to an all (or mostly all) player run shop system, that's going to really limit my ability to plan out projects because I won't know what items I can count on getting, what prices I can expect to have to pay a month or more down the road, etc.
4.) I really don't want to have to look in 15-20 "shops" to find a supply of something. I'm lazy - I like one stop shopping. If the new system doesn't have some sort of inventory search, it's gonna drive me crazy... and I'm taking all of you with me!
On a more serious note -
As a builder, what I'd like to see is a shop system like we have now, with additional player-ran shops or auction system (like World of Warcraft auctions) to run concurrent with the server shop. As a builder, nothing else would be acceptable to me (when I'm trying to do large builds).