Yeah, I don't quite get how someone as good at world-building as Bethesda can be so bad at actually telling their story. I mean, writing is writing, right?
I think the problem is that A: All the really really cool shit happened in the past, and it probably wasn't as cool when it was happening. And B: the game is a sandbox. It's supposed to be non-linear and have fairly high player agency. This is not conducive to telling a story. It's good for allowing the players to make their own story and have their own experience, but it's terrible for allowing the developers and writers to tell a story. There are a few ways to fix this: The Farcry 3 method, for example, is gradually opening the sandbox as the player progresses through the story, and not allowing the player to interact with the really important elements of the story until it's time for the player to play with those elements. Another method is allowing the story to branch and create different story lines based on player actions. This is difficult to do well, especially in a series where the events of the 5th game are based on the events of the 4th game. Having so many options for how the storyline will progress is why Bethesda had to create the Dragon Break - there were so many options for the end of... Arena? Daggerfall? One of those, that in Morrowind(? I started with Oblivion, so I'm not too sure of that), they had to deal with the multiple endings somehow. They elected to take a third option and declare every possible ending as canon. This is not really a great way of doing things.
Sandbox games are probably never going to be a great medium for telling a specific story, because by their nature they allow the player to subvert the story.
Oblivion was an attempt to tell a better story. The story progression for morrowind was pretty ideal for a sandbox game, in that you have to take the story slow because the difficulty of the sandbox made quick progression too difficult. That is, much of the sandbox was off limits to the player, but by the enemies you found there. That means forcing the player to do side missions and explore on their own pace, putting the story second. It made for a fun game, but a poor story, although the history behind the story is interesting, (I also have to agree that missions in bethesda games, and many sandboxes amounts to "go here, kill this, retrieve worthless item X").
Oblivion was different, the story was more engaging, and the quality of the sandbox suffered to enable the engagement, ironically two separate things players complain about (myself included).
I think the fundamental problem with the story writing for TES is the nature of it. More often than not the story in the game creates major holes that need to be fixed, and any attempt to do something creative is more likely to upset established players than make them happy. Its a no-win scenario.
On the one hand, I would feel sorry for them, on the other hand, I am forced to hate them forever because of the gimped magic system in Skyrim (and Oblivion too, but there were ways around that). But also, I have a hard time respecting a development team that admits they can't figure out ladders. The people who brought you Duke Nukem Forever, and Aliens: Colonial Marines figured it out, buck up.