I'm not saying they have to hand craft every single dungeon but at least make something different. Every for in the game looks like it was designed by the same contractor! My god couldn't the soldiers have changed the wallpaper, carpeted the place, put a slipknot poster up? SOMETHING to change the look and make a place look unique?
One of the reasons they looked like they were made by the same contractor was because they were all made by the same contractor, or, more appropriately, designer. Furthermore, I completely agree with you on the fort quests, I hated them, avoided them when I could.
I agree w/ the OP in that it seems strange, if you were to take a layer by layer view of Cyrodil, it would undoubtedly look like an ant farm, tunnels moving all over the place, and, due to the miracles of not-actually-having-to-engineer-in-reality-where-space-exists-physically-in-only-three-dimensions, a designer could literally have two dungeons in the same place if Cyrodil was a physical manifestation.
This being said, if these networks of tunnels were to be suddenly brought above ground, Cyrodil would no longer look like an ant farm, but more like an extremely ruinous labyrinth, take even half of these ruins away and you have a very large and fairly easy ruinous labyrinth, it's just not practical to have them above ground and it's just not realistic to have them below ground. So I say, put them in outer space! Then you can ride your tamed dragon to the orbital wolf den to retrieve some woman's aunt's dog's carcass... IN SPACE!!!
Alternatively- compromise, put as many above ground ruins as feasible, and put the rest below ground. SOLVED.