Don't get me wrong, the Dark Brotherhood in Oblivion was perfectly fine, but it just didn't stand out to me. The Thieves' Guild did. The Dark Brotherhood did a lot of filler quests that, really...I would argue it wasn't how they were WRITTEN that made them fun, but rather the game design that made them fun; the Dark Brotherhood was fun because you had like 4-5 different options on how to complete the mission and the rewards were sweet, NOT because it was especially well written. The Thieves' Guild on the other hand, everything related to the main quest in some way; there was some filler, sure, but it was sort of a package deal and a sub-plot (as in if you did a quest for the Thieves' guild, it either related to it's main storyline or to a sub-plot; there was ONE sub-plot, not multiple random fillers), rather than just random filler going in every direction.
And while the Thieves' Guild kept you guessing until the ending, making you question what the HELL the Gray Fox's motives were while also encouraging you to play along with him for the sake of the glory of it, going down in history as one of the greatest Thieves' ever, the DB questline sort of just suddenly said "btw here's our overlaying plot as we introduce you to act II." Then you enter Act II and again there's tons of repetitive filler not nearly as fun as the ACT I filler amongst the sanctuary, and then a problem is developed just as quickly as it's solved.
To me, the Thieves' Guild did it better. The Thieves' Guild elegantly introduced a couple mysteries to you at the beginning, then unexpectedly tied them all into the plotline, so you got more answers than expected. The Dark Brotherhood's story arch was a little late to the party and failed to tie into any former mysteries or anything really; it all happened within the Dark Brotherhood.
There's a design saying for games in general that says "make it look hard, but play easy" as a way to satisfy people. It's somewhat of a stretch, but I believe the Thieves' Guild was considered so successful because it matches this philosophy in the sense that you had modest, reasonable expectations, but it delivered MORE. The only mystery we're expecting to solve is "who exactly is the Gray Fox." This is our reasonable expectation. By the end though, the Thieves' Guild delivers that AND the answers to several other mysteries on the side. We find hidden meanings behind almost every action we've done. In that sense, I consider it to be one of the best pieces of writing Bethesda produced; perhaps THE best of the three I named.
The Dark Brotherhood, I think was done decently enough but tbh if I'm critical, I think it deserves more criticism than approval. As I said, the Dark Brotherhood's story is late to the party, so for a while we're just enjoying the gameplay, not the story. We HAVE no reasonable expectations of the story because they haven't really given us one. Then suddenly a story reveals itself, and after one mission, it disappears again. Then another ~7 missions later, it pops back up. They could've very well have tied the main story into ANY of the quests we did at that point; we had little reason to believe that ONE we did in particular was pivotal to the storyline. Suddenly we're told "no it was pivotal" and sent to fix the issue-that-we-apparently-haven't-solved-yet and before you know it, we've already solved the problem and the faction is completed.
Likewise, the College of Winterhold as an example receives scathing reviews. Why? We're introduced to dozens of characters and themes, but by the end we know nothing. Our reasonable expectations are to know wtf is going on, wtf that thing/guy/blob is below the college, wtf was the point of the little scenes involving a young arch-mage, what the villain's motivations were etc. In the end though, it delivers none of this.
Again, that the Oblivion Dark Brotherhood was held in higher regard by Bethesda than Oblivion's Thieves' guild? I can only attribute that to falsly attributing the DB's success to it's storyline. No, it's quest design was the best. DB had the best quest design in the game, but not the best story. The Thieves' Guild writer should've been the one that got promoted to lead writer whereas the DB quest-designer should've been promoted to lead quest-designer.