I thought Bethesda did a much better job with this in Skyrim than they did in Oblivion. In Oblivion dungeons didn't feel like they were an organic part of the landscape to me. I rarely felt I was in the middle of nowhere in Cyrodiil. I could almost envision a memo arriving from the front office, specifying: "One dungeon per exterior cell, no two of the same type of dungeon right next to each other." It felt mechanical and contrived to me: one Ayleid ruin, one cave, one mine, one fort and then it was time to cycle through the dungeon types again: one Ayleid ruin, one cave, one mine, one fort.
In Skyrim I find myself looking around now and then and wondering where the dungeons are. I find myself thinking, 'Wow, I'm really out in the middle of nowhere here. There's nothing around me in any direction. I haven't even seen a wolf for the last ten minutes.' The placement of dungeons in Skyrim feels as natural to me as the dungeons in Morrowind felt. I consider that to be high praise.
I think the landscape of Skyrim is very well suited for natural dungeons such as caves and they are integrated with stunning artwork. The forts and barrows of ancient Nords also provide excellent dungeons that are completely natural to the overall feel (though there are too many forts IMO). At any rate, Cyrodill is a very bland landscape in and of itself and maybe that's why the dungeons felt mechanical and bland too. I would love a Skyrim-graphics reworking of Cyrodill though, just for the cities (the Imperial City could be made simply stunning now), maybe they could have less dungeons and find a way to integrate them more. That said, I'd much rather have a province like Elysweyr, or High Rock be the subject of the next installment in the series. That reminds me of an awesome Skyrim mod where a guy is actually making Black Marsh. The project is still in it's early stages so there's two deserted towns, a few locations and two populated forts, though the only characters that have more than basic interactions are vendors.