A strong stats system, a good journal, believable guilds and guilds questlines, a mature and complex dialogue writing.
Adding up all the parts, it seems Skyrim has all the elements to make it every bit as good as Morrowind or Oblivion. But as you pointed out, there are some key things that are either totally awol, or pretty weakly implemented. It's as if there was a huge bull session at Bethesda, and everyone got a chance to throw ideas down. Great, some good ideas, some not so original, but they work on paper.
So different folks worked on different aspects and stories, but it does not appear anyone saw the importance of having a single narrative style used, in order to connect all the miscelllaneous dots. YOU are the dovahkin, so how do the guilds view you? How do your primary adversaries ( oh there isn't one, save Alduin...) react? How do the leaders of each hold, or each guild acknowledge you. Why aren't you the "Savior of Skyrim" if you defeat Alduin? Help one side win the civil war? Your path is cleared a bit to becoming a Thane, and buying houses, but there's no siginificant acknowledgement by anyone. Indeed, many of the townfolk prattle on, as if Ulfric or Tullius were still out there threatening them. I could count numerous examples of AI being stuck in a info vacuum, but suffice it to say the game world doesn't seem to progress forward in real time like earlier ES entries did.
I know there were those who grew bored with the duration of the questlines in Oblivion, but shortening them to the extremes we see in Skyrim was a serious mistake. There is little opportunity to connect with the leader of the companions guild, or the mages guild, certainly nothing to the quasi -relationship one experiences with Modryn in Oblivion. And relying on random generated quest objectives, cuts out even more of the background story and depth, while highlighting the reality that they are re-dundant and/or repetitive.
Skyrim is hollow where it's heart should be.