I felt the Thieves' Guild was the biggest let down with a truly broken story.
It isn't so bad. I'm not going to give spoilers, but while you being made the guild leader didn't make complete sense, at least it wasn't so contrived as the mage and companion quest lines. What bothers me about the Thieves' guild is that even as the leader, everyone still treats me as if I am the new guy. The quest line is buggy, too. I was never able to get my guild master armor, never got my key to the treasury, lost the option to train with some of the members, and one quest never gave me the reward. Meanwhile, I had a sub quest to take care of someone's debt which stuck in my queue even after I killed the guy. I had a miscellaneous Riften quest that had me talk to Sapphire, who still acted like someone else was the guild leader. Everyone is also swimming in the cistern whenever I'm down there, and I've never been called on to do anything more for you-know-who even though it sounded like I was going to be called back from time to time. It's like they never finished it.
The Companions quest line is ridiculously short and hurried. Your ascension to harbinger is so fast and absurd, that even your guild members complain about it! You're let in to the guild's big secret--that even most guild members supposedly don't know--almost immediately. You're inexplicably inducted into the circle after what barely amounts to errands. There were miscellaneous quests longer and more involved than the Companions' one, and I felt zero sense of belonging or accomplishment.
I've done all of them on various characters, and I can say with a fair degree of certainty that the guild quests were rushed in so they could meet their 11/11/11 deadline in the following order: Dark Brotherhood, Thieves' Guild, College of Winterhold and Companions. In my opinion, the Dark Brotherhood has the best guild quest line in the game.
It's all a far cry from Oblivion, though. Going on any of the guild quest lines was a major investment in time. They were long, not at all rushed, and at the end you truly felt like you accomplished something. It's all very much dumbed down in Skyrim. If Bethesda spent as much time on the main/guild quest lines as they did on the miscellaneous quests (you can't swing a dead skeever without hitting someone who wants you to do something for them) and the beautiful game world, Skyrim would go from "fantastic" to "perfection."