I don't think you'll be limited to one store. It seems like a fundamentally bad idea to rob the same store over and over again. If you were to ransack a weapon store clean, I think that would put one hell of a dent in their business, certainly enough to put them out of business. There should be good stuff to steal this time, but at the same time they need to offer more repercussions, other than "you're under arrest for X amount of time"

If you rob from a merchant multiple times you should walk in one day and see him/her hanging from the rafters while their spouse and children are crying hysterically in a corner!

Well NPC can recognize items they cell and thats items was stolen from them and player trying cell this items back to merchant like in Morrowind, but also NPC can make check of player equipped items and if say if item was stolen
Item can be marked as stolen as long enough depending on price of item, stole an apple or stole crown jewels to understood the difference, previous owner of item can recognize his stuff always.

NPC can hire security from Fighter Guild to patrol their shop and get rid of thieves, I'd like how NPC react in oblivion if player sneaking around or trying drag item somewhere, but thats can be tweaked more like in this mods
Put it in its Place - Enhanced Grabbing
http://tesnexus.com/downloads/file.php?id=19847
Reneers Guard Overhaul
http://tesnexus.com/downloads/file.php?id=5977

Merchants have secured storage with goods they are sell, its located somewhere in shop locked and can be guarded, merchants not allow go to storage and thats is work like trespassing.

Merchants change broken locks if they was bashed or someone stole keys from shop owner after some time (3 days like before for example) like in this mod
Reneers KeyLock Mod
http://tesnexus.com/downloads/file.php?id=33630

Merchants shops must have closing and opening time and this time can be different some mystical shops for example can be opened in evening and night, closing time can work with their daily activities well, thats part of Radiant AI, player can ask merchant about his work schedule.

NPC can be aware about player fame/infamy count and change their service accordingly, lawful and confident merchants can even refuse to work with shady mans
Merchants can bye stolen items if their disposition toward player is high enough and they confidence not very high.
Friendly Merchants Buy Stolen Items v2
http://tesnexus.com/downloads/file.php?id=31820

Merchants can give player quest like in Daggerfall or this mod
Enhanced Economy
http://tesnexus.com/downloads/file.php?id=25078
Thats can be awesome part of Radiant Story system

Definitely there must be traveling merchants like in this mod
Tamriel Travellers 139c
http://tesnexus.com/downloads/file.php?id=4387

Seems kind of silly for them to raise prices... people will just take their business else where.

Two Worlds 2's system was neat. The more of an item you sold to a shop keeper the less he would pay. Basically like if you saturate the market with a certin item it's value is going to drop. It could get annoying at times when you have 20 of the same sword and after selling 5 or 6 they arn't worth much anymore. But in that game you could break them down and use the parts to upgrade other weapons...

awesome ideas' and a lot of effort. It would be awesome if say you are in the fighters guild and the shop hires you to stop thieves. Another thing is that if you are sneaky and you are a master thief as well in the fighters guild,you can be employed as a guard but then steal everything from the shop, but you will never be employed by that shop again.

It is likely you would get kicked out of the Fighter's Guild as well.

Guys, if you rob a store the next time you walk in a five year old child should point at you and say, "You did this!" before kicking the chair out from under them and hanging themselves.

I think I really like this idea over a blanket stolen/not stolen system. If you are a known thief, anything you try to sell should raise some flags around honest merchants. "Sure the last three times I pawned off stolen merchandise on you, but this time is different! Honest!"

THIS.

I thought it was too easy to take a castle blind. If they MASSIVELY increase the security presence in castles and add in a system that replenishes stock (in other words, markers that generate items so they keep re-appearing on the shelves) as well as posts a guard inside the shop for a week or so after you steel from the store, that would make theft much more challenging and much more fun.

I think local crime rates affecting the prices and availability of goods would be ( irritating ) but realistic. Ransacking a shop or robbing a trade caravan should affect the economy.

Stealing from a shop multiple times should just have the consequence that the shop upgrades it's security, either through more guards or guards doing random searches of costumers who walk out.