It was done that way because the easiest way to get rich quick in Morrowind was to steal every fork and spoon and then just sell it to all the traders in the world. When a trader would run out of money, move to the next one.
Fences "balanced" theivery so it wasn't so easy to get-rich-quick but made it a big pain in the ass to do, PLUS broke the 4th wall (how would anyone know I stole this fork?). Plus once you realized you could just FT to the fences, suddenly it was easier to get rich in Oblivion than it ever was in Morrowind.
So how could skyrim get rid of that 4th wall breaking, but still not be as unbalanced as Morrowind?.....
In Skyrim they need to make it so vendors will flat out not buy certain goods more often, or only buy if in certain conditions.
Such as, if they have lots of money or any money and you have a rare item, they'll almost always want to buy.
If they are poor and you try and sell them a common item, even if they are a vendor that sells what you are selling them, they should decline. If you try and sell them a common item at all there should be a much less likely chance they'll offer to buy it even if they are wealthy. ESPECIALLY if they already have that in stock.
So theives would have to play smart. Steal things of value, and steal diversely. Don't steal too much in one town because then people will be too poor to want to comfortably buy your goods. If you steal too many common items no one will want your stuff unless they have money and are low on said commodity (like food, plates, etc). If you rob a town blind then no one will want to buy as they'll be too poor.
They could also make it so some vendors only buy in certain days. Like a pottery shop owner will only buy in mundas or something.
They could still have fences, for those REALLY valuable items that you want to get a good buck out of. Or for illegal items. And they'll buy anything, but they shouldn't be common... i.e. have a fence only appear at a certain meeting spot at a certain time of day to do business.
And how about they tie it into the Radiant Story? Make it so one doesn't show up in town unless they feel like they can get good business there. So unless you have a history of skillful theiving or have direct connects to the theives guild, a fence might not even appear in the town you are in.