The cities in Skyrim feel so functionally "Cookie-Cutter" because a lack of a legitimate market within them.
Take Balmora from Morrowind, having 3 General Stores, 2 general smiths, A bookseller, an alchemist, a tailor, Two inns/cornerclubs. This doesn't even factor in Guild merchants.
Even Oblivion's Imperial City was believable in that sense.
Compared to Whiterun? 1.5 Inns, 2smiths, 1 general store, 1 alchemist, and a handfull of market stalls. And this is supposed to be the Central "Trading hub" of the province.
I'm not saying Skyrim's cities couldn't have been made better, but it's not as bad as you're making it out to be.
As for comparisons to Morrowind, lets just be real here. Morrowinds cities had different varieties of buildings, but within each town almost all the buildings looked exactly the same from the exterior. Add in generally cookie cutter interior designs and NPCs that generally stood in one place, had no voiced dialogue, and could be given the same text dialogue as every generic NPC in the gameworld. Morroewinds towns were great for their time, but I don't think it's hard to see why it wasn't as practical to put 2-3 of every type of shop in every town in Skyrim like it was in Morrowind.
I agree that the Imperial city itself was larger and offered more variety than any city in Skyrim, but that makes alot of sense considering it's the capital of the Empire, while Skyrim is a less populated province of people who like to make a living for themselves in their rough surroundings rather than trying to form international trading hubs in their cities.