Was there some inherent limitation to Skyrim that prevented the devs from making a city that can be compared to Vivec City, Imperial City, or Mournhold?
Don’t give me that quality over quantity BS, almost all Cantons in Vivec had a good amount of content. Especially the house vaults

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Well first off, let me say I'm a really devoted fan (no word filter A FAN BOI) of Morrowind.. but now lets take a step back..
If you have any mod (you're playing morroblivion, so that should work) that gives you the ability to see more than 100 yards without some unfortunate fog blocking your view, you should be able to tell that Vivec honestly wasn't that big. It was spaced out, but the cantons were tall if anything, and the outside details weren't that vivid. Also the insides are interior cells.. they have nothing to do with the "size of the city". Unless of course you're comparing the interiors of a city (houses, jarls house, underground areas) to the entirety of the inside of Vivec. If THAT is the case, you're right, Vivec as a whole had more (canols).
If you have already taken a step back, great.. if not do so now.. Oblivion came out for the 360. It had the Imperial City, which although not HUGE, was still pretty dang big. Granted it was sectioned off and each section was its own cell. Skyrim also came out FOR the 360. It easily outstrips Oblivion visually, and it should be understandable that the cities aren't going to be nearly as large as the IC (even though honestly some of them are still quite large.. Solitude? Markarth? Windhelm? Whiterun?) But here are some things the cities have in Skyrim that Morrowind doesn't. NPC's which are more than reservoirs of repetitive text that have day/night routines and go to pubs and the like. Effects! They have weather effects, smoke, and Whiterun they have the cutsie wootsie little hay straw things floating around

. Exterior objects out the wazoo.. Whiterun for example, forges, fencing, insane architecture with dragon heads carved into beams and a flipping tree garden thing with a stream forming a circle around it.. Solitude has way more.
I'm just saying (I just woke up so if there are some glaring holes in my arguments, forgive me) Vivec was cool, but can not even possibly compare visually or technically to even a weak city in Skyrim.
This coming from a huge fan of Morrowind. Now if you were to compare a city in Skyrim to that of Mournhold.. but then again that was an entire DLC expansion

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the cities are horrible, we didnt even get the many NPCs we were promised for the loss of greaves

I remember fighting a LOT more NPC's during the civil war quests personally.. it's nice to fight more than 4 enemies at once (that aren't cliffracers.. )