I hate the blades. Delphine is a bit** and Esbern is a fool. Just sayin'. They want you to kill paarthurnax (really made me mad that you couldn't tell em no, or kill them instead). They are arrogant. Delphine thinks she can take ME on? Pfft. They don't want to help, they want to control. I've never hated a faction more in Skyrim.
The Dark Brotherhood was a fun questline, but it made me feel bad for killing some of my targets. Narfi almost tipped the scale in favor of destruction. Not only that, but most of the members die. It doesn't stop there, you are FORCED to interact with the thieves guild. Complete bull imho.
The thieves guild was also fun, but got tedious and annoying very quickly. You are forced to go to them too many times (I consider even once to be too many). They are arrogant, and also force the dragonborn to swear fealty or whatever to Nocturnal. That's bull. It also makes me mad that some of the dialouge makes the character sound afraid of the boss of the storyline.
The companions was fun, no real complaints other than forcing you to become a werewolf. Also, you had no choice but to avenge Skjor (I think, I never tried asking other members for work at that stage).
The thalmor get rude and annoying, but I don't hate them because I understand there needs to be an antagonist in every story like this one. Not to mention, Bethesda didn't do a good job of making me hate them. Fighting them was something we're forced to do (stupid Delphine) and the only other motivation is the XP. Really didn't do a good job of making it personal.
I'm concflicted between Stormcloaks or Empire. Their questlines feel incomplete at best.
The college of winterhold was fun, but there was no way to say "screw you psijiics" as I hate being manipulated by some people and not having any choice in the matter.
The dawnguard and Vampires were pretty cool, but you get pretty much all of the rewards for joining Dawnguard, and miss out on so much more with the vampires. No real reason to join the Vampires other than role-playing.
Solsteim is a whole other creature altogether. (Go Reiklings!)
Almost forgot to mention the lack of hate for vampires on the dawnguard side. There are a few exceptions, but for the most part it is just running around with Serana until the big battle. I'd expect a lot more from people supposedly as dedicated as the Dawnguard.
The Vampires introduced lots of good ideas, like the side quest of turning your spouce into a vampire and etc for role playing purposes. Most of it however, was too glitchy. I alsp don't like how you get pretty much the same amount of hate for vampires from them as you do from the Dawnguard (you still go hunting for vampires and STILL turn on Harkon).