Few problems I see with the current shops:
1) People don't understand how to use it, so they get frustrated and start complaining.
2) There are more steps to sell one item in shops then in a chest shop, Time is money! (slower if you are only selling one or two stacks, but quicker if you selling more then 4 or 5 stacks.
3) Selling quantity, you need to put a specific quantity to sell, which gets obnoxious to try to count up everything you have. It would be nice if you could put for quantity -ALL or a larger number than you have, but you would only sell what you have in inventory.
4) Older players liked having /sell so they didn't have to warp to shops then go back.
5) Shop is in Spawn, and spawn tends to be laggy.
I don't think the shop is as bad as people say. I think with a few minor adjustments, it could run smoothly.
~ @DET2102
I apologize, I was thinking the server shops, not chest shops.
Reading is not only fun kids, its fundamental.I followed these guidelines (from http://dev.bukkit.org/bukkit-plugins/chestshop/)
and I haven't experienced any problems.
Place a chest on the ground
Place a sign 1 block away from on the chest (for example, above it)
On the sign, write:

First line will be filled by the plugin automatically
Second line is item amount (quantity)
Third line: Price line is a combination of buy and sell prices.
You need to have a price indicator (like 'B' - price that will apply to items BOUGHT by PLAYERS - or 'S' - the SELL price) near the price - the prices are separated by a colon :))
Last line you use item id number.
Some of the possible price combinations: "B 5:5 S", "B 5", "S free"
You can find out the name of the item you're holding by doing /iteminfo
When you are done, you should be prompted in chat with:
[Shop] Shop Successfully created!