Skyrim took great strides towards giving players more unique content to find in dungeons - especially when you compare it to Oblivion which had almost nothing unique in most dungeons.
Very true. There's a good chance that any place you enter will have some sort of story element.
Skyrim's biggest problems with story seem to be due to cut content and a general lack of consistency amongst the designers regarding the lore, particularly when it comes to timelines (Dawnguard's a complete mess). Regardless, it's a vast improvement on Oblivion, and I was pleased to see the Shivering Isles ending stupidity was largely ignored. Too bad they didn't drop fishmalk Sheogorath, too.