Hard to choose only one. I suppose I'd have to go with the writing considering it feels as if its all written by a headless turkey when it comes to Bethesda.
The lack of character depth. NPCs have become less resourceful since Daggerfall.
EDIT: The lack of mountain climbing animations.
The sea was done better in Skyrim than it was in Oblivion.
The lack of true classes. My barbarian should not be able to also become an arch mage.
That your in-game decisions don't affect the rest of the game.
Far too easy to become guild head in all the guilds!
Some very lazy writing!
Yep. But at least climbing mountains is always fun.
Probably the terrible AI, but I could live with that if the primary questlines (DB, Thieves, etc) weren't so ridiculously linear and forced you to make lame choices. You *have* to become a werewolf to finish the Companions questline, you can't destroy the thieves guild, and you still have to murder someone to destroy the DB.
I don't make characters who belong to more than one guild, but in Skyrim anyone can cast a spell and that's all you need to get into the College of Winterhold.
Casting one crappy spell that they offer to sell you for like 50 gold? Considering you get a +30 magicka hood in the tutorial quest and can easily get a ring or necklace to boost it a little more, casting that spell to get in is a pretty low bar to clear.
Some of the quest as you moved on should have required you to have a 50 or 75 in one school in order to progress, with them telling you to "train more" or something in order to continue. If people want to grind their skills up by casting soul trap on a corpse or whatever to progress, well, then thats on them.
Skyrim is a mile wide but a foot deep. That is my main gripe with the game, everything feels shallow/hallow. NPC's are robotic and I would like to have followers with actually depth, Serana is a step in the right direction imo. Other than the hallow feeling skyrim has, I still enjoyed my time with the game.
Grelod the Kind may not be a nice person, but you still have to kill her in order to progress.
This is my revised biggest flaw. The lack of climbing animations!
Removal of attributes, removal of armor and weapons degradation and repair hammers, quests not having consequences depending on the choices you make and not having branching paths and more than 1 dialogue options, adding regenerative health, keeping the essential NPC's since The Elder Scrolls IV: Oblivion, and the quest arrows, markers appearing on your compass and map.
I agree with all of the other flaws posted here already. One that consistently pisses me off is the lack of player recognition by the AI. The guards who say, "Did someone steal your sweetroll?". I am your thane, leader of the companions, Archmage,... (insert other titles) or possibily even just a high leveled monstrosity. I have to try really hard not to teach him some respect and Fus Ro Dah him to his knees (at the bare minimum).