I haven't finished the main quest just yet; been exploring and doing some of the deadra quest. Mehrune's Dagger for my Night Assassin.
I have done the Thieves, The Companions, The Mages, and the Dark Brotherhood guilds.
If I had to rate them. The College of Winterhold, Dark Brotherhood, Thieves, Companions. [and my scale is based on impact on the world, which none of the guilds actually had]
I hate being forced into being a werewolf or the fact that I hadn't really earned the right to know their secret. It would have been better if let's say they had Oblivion style quest. After doing those errand boy quest for the mages guild darted across the land only then could I go to the college. Then even then in the college I was running as an errand boy and actually earning my rank as an apprentice. Not one quets and suddenly I'm an apprentice.
After a while the guilds in Oblivion were so long and so hard and tedious I actually hated doing them sometimes. Because I was nearly dead and then I was like I have to report to this dude. Bah humbug. lol. I actually felt like I was being sent out to danger and even ranted to the arch mage about how I hated him, how I'll never do his quest again and yet here I was doing the quest.
I hated how in the Dark Brotherhood in Skyrim
had no real impact. I remember in Oblivion doing the Thieves Guild and I cannot remember if this happened in the Dark Brotherhood as well, but in Oblivion you'd hear towns people whisper of the deads. "Did you hear the Elder Scrolls has been stolen?" and it was even on one of the newspapers too, some courier just gave me a newsletter and I read about the Elder Scrolls being stolen. That had some impact on the environment.
The guilds and questlines, all though good, decent enough for my attention had no real impact. Or inclination that it had an impact.