The copy paste caves. And ruins did suck though
I was always torn with the ruins, as I really liked the look and atmosphere of them, but if you've seen one then you've seen them all. They should take a leaf out of Bioware's book in regards to the identikit bases in ME1 that were outside of the storyline; in ME2 they severely cut down how much you could explore around the galaxy but gave each area a much more focused, unique feel.
Then again, Bioware and Bethesda RPGs both have a very different agenda, so using the design principles of one doesn't really transfer to the other. Bioware RPGs are far more focused and story driven, whereas Bethesda really want you to create your own adventure, and to do that they need to create a huge world populated by a ton of stuff to do. To that end, it really wouldn't be feasible to create a world as large and detailed as Cyrodiil by hand, the man hours and production costs involved would just be insane. Games like Uncharted and Call of Duty can do that because they're so linear, whereas Oblivion and Fallout allows you to explore every nook and cranny at your will. Occasionally it is inevitable that some nooks are copypasted and some crannies just don't live up to expectations.