Comparing the guilds to Oblivion, yeah they were short, too short.
The Companions- The storyline was just plain and simple, dumb, boring and left a "WTF was that crap?" moment in your mouth.
The Bard's College- I would not even bother calling this a guild, more like a waste of space in Solitude and pointless being in the game.
The Mage's Guild- Uh, comparing this story to the one from Oblivion, I have to say I was not impressed at all. I am still trying to understand why the Arch-Mage looks like the devil.
The Thieves Guild- Not bad, not bad at all. Could have been a bit longer.
The Dark Brotherhood- Not sure on this one, at some points I enjoyed it and other points not so much. I am disappointed seeing the issues people had with the aftermath of the Dark Brotherhood were not taken care of in this game. Furthermore I hate the Night Mother's voice in this game.
I miss that climb the ladder and the on the edge of your seat feel with the story lines. While it seems the guild quests were handled with care in Oblivion, the guild quests in Skyrim played out as if they all were done over lunch one afternoon.
Sure, sure, the side guild quests are nice to have, but you can have side guild quests and a good long main guild story with no need to sacrifice one or the other.
A guild should be all about getting to that top spot but once your there feel like your character did earn it, instead of this feeling of earning it without doing much of anything. At least the Thieves Guild does this, shame the other guild's did not follow suit.