Followers being able to die (Very hard, and a minor issue) is the most recent one, I also really don't agree with the magicka cost for almost all the higher rank spells, as they seem to be tuned to be almost completely unusable without either a retarted level of caster building or the 5 points in EACH magic tree for the half cost, 25 frikkin perks (Which is HALF of what you can get in the game at the soft cap). Hell, some of the coolest end game spells like the thralls just flat out cost too much mana to cast even once without those perks unless again, your sinking a collosal sum of extra magicka/cost reduc into your gear, its a frikkin huge buzzkill for my spellblade.
All of those things are minor gripes compared to the perk system itself. That thing is the blight of my existence. They took out automatic benefits of levelling skills in oblivion, stuck them into a shitty skill tree, and then give you about 50 out of the 220 perk points you need to get them all, so again if your a hybridish type that likes to dip into alot of skills, you get to eat shit

.
I stand by the fact that if they just gave you a single skill locked perk point every 20 levels of that skill, the system would be perfect. You would get 5 points, and most trees only have around 10, just for actually buckling down and raising the stat, and then use your actual level to bolster the really important ones.
As it stands, it just makes me not ever want to raise anything but the most vital skills because they are gonna suck ass since I can't perk them anyways.
For the record I still give skyrim a solid 8/10, and I intend to play it for a decent while, atleast through december, but really, they couldn't atleast add a damn respec vendor? It's diablo 2 all over again, which was a nightmare -.-.
Edit: For the record I am told by my elder scrolls nerd friends that my issue with perks is about 20% valid and 80% diablo 2 induced emotional trauma. I am considering that possibility internally <.<. In my defence, it doesnt take 300 hours to do a diablo 2 playthrough.