There have been some very intriguing and smart stories told in Bethesdsa games. Perhaps one should not look only at the MQ, but also side quests.
For example in Oblivion, the story of the Who dunnit quest, and the overall arch of the Dark Brotherhood was awesome story-wise IMO. The story of the Gray Fox as a person, I find it great too. Paranoia was another awesome quest that was awesome just for its plot.
Fallout 3 too had some quests that I really liked story-wise. The one where you get trapped in the virtual world, the tree-man, the conspiracy to blow up Megaton... These were good story pieces.
Then came Skyrim, were quests for some reason had all to be written around the same gameplay mechanic of fetch quests, and killed it.
Looking at pre-Skyrim Bethesda games what I find is that there are MANY good, interesting stories in them. The problem with stories in pre-Skyrim Bethesda games has been not in the stories themselves as stories, but in the way they are presented to the player and executed. You know what ? No matter the medium, be it game or movie or book, what makes us enjoy a story more is to get to feel like how the characters feel. No matter how good a plot is, if the actors are bad and bland and the direction is bad, people ain't going to like it.
Look at the Mass Effect trilogy. Up to before the end of Mass Effect 3, everyone loved its story, and many people were saying that the games were the best regarding story. If you just read the main plot though, you will discover that it has nothing groundbreaking in story telling. What made people love ME and think its story is great, was the fact that Bioware managed to make the player care about the characters. And for that to happen many factors had to be right and played a part. A big part of making someone care for characters is to understand their feelings. All those face-close ups in the classic and awesome Spielberg films, are done for that particular reason: to make us understand how the character feels at that point, whats in his or her mind.
But how can the 'rules' be applied in video games ? One thing facial animations. Since a great amount of information about how a character feels is communicated by his face, being able to see the emotions reflected on facial expressions on characters is important. Look at the few games that used motion capture of real actors to capture their facial expressions / feelings and put them in, like everyone in LA Noire and Vaas in Far Cry 3. The main story of Far Cry 3 was rather bad and cliche, but Vaas saved the whole game and made it special. While everything else story-wise in Far Cry 3 was bland and boring, Vaas kept us interested in playing the game, and lots of players quit playing the game at the point Vaas died.
Why ? Because Vass had a personality, and not only that, but both is animations and voice acting were taken from a good actor, that managed to play the role good, and thus we were recieving tons of information just by the combination of the look in Vaas's face, the tone of his voice, and the movements of his body. The combination of these three made Vass interesting and immersed us.
Little details like how he closes his eyes right when he says "I don't like the way you are looking at me", and how he moves his arms and fingers when he says "f**k you ok!" in this video:
https://www.youtube.com/watch?v=7n_1zsCVBxw
might be small, but have a huge impact on the player. Because the body language and expressions and voice tone are natural and their orchestration makes the whole outcome rather natural and realistic,and that makes us suspend our disbelief, which allows us to see Vass as a 'real' person somewhat. Thus we grow feelings about him,
and that keeps us interested in seeing how the game progresses.
Another thing is good, emotional voice acting. To use audio as a vehicle to transfer the feelings of the characters to the player too. And of course camera direction plays importance.
So this is what I think. Only in Skyrim I found a lack of interesting stories. But in past BGS games I found lots of interesting,good pieces.
The major thing with story in Bethesda games IMO isn't the writing itself, but the way the stories are presented to the player.
To break it down even more, Bethesda needs better in quality and more frequently used facial expression animations for its npcs, more emotional voice acting, and have the NPCs show full proper behavior depending in the situation they are into, and by behavior I mean their bodies, to communicate the right things with their body language.