Well, in Morrowind it all made sense. Caves are made by nature. Mines are made by men. Daedric ruins are made by worshippers or even of Daedra themselfes. Dwemer ruins were made by the dwarves. In Oblivion they removed the daedric- and dwemer ruins and created Ayleid ruins - also made sense. But they also created the common "ruin" that looked like a big tower or a little fort or something like that.

In Skyrim they even extended that and those ruins sometimes even look like small citys with courts or fortresses. Now I wonder... since we actually play in (fantasy) medi-eval... who built this? I mean it's not something that is hidden from us.. it was obviously built by men but how? Was that in a time when some duke or count could just built something of their own. And why does it happen that all those buildings are abandonded, destroyed and re-populated by thiefs, thugs and necromancers? Why are there no still-in-use forts?

(I know, it's a gameplay thingie, but still it bothers me)

In Skyrim, there are. You can also recapture some of them from bandits during the Civil War campaigns for your faction's own use. And yes, they're simply the ruins of old fortresses and old cities that were build by the Nords or even the Empire.