The story has never really driven people to love TES, it's the exploration and freedom the games allow that gets people to eat them up. That's not to say that a really well-done main storyline can't be appreciated. When faced with an entire country of stuff to do, a 4-hour main quest appears pretty lackluster and the civil war doesn't seem to have any noticeable effect apart from who the Jarls are. By the nature of a game that emphasizes freedom, it's not exactly possible to tell a story along the lines of Bioshock or Silent Hill 2 where you're forced down a pretty linear chain of events, but then games like Ultima were able to have great metaplots without sacrificing where you can and can't go. A story like Dragon Age: Origins, which mostly involved running around between civilizations and trying to get their support, could have worked perfectly in a game like Skyrim. Better than it did even in DA:O, since it's lack of an overworld really hurt the scale of the game.
As for dungeons, frankly, get boring after awhile, barring of course when there's a twist thrown in like I mentioned before. But most often they're a generic slog through samey caves, crypts, or temples. They get tedious. And while there are hundreds of them and you can say that there's no way they could have made each and every one of them unique, it's true but that doesn't mean there still isn't a lack of variety. There's exactly one puzzle present in dungeons: Match-the-animal. Every puzzle is derived in some way from that, and it can be as easy as the correct order of the animals being shown to you (and really, what's the point of the puzzle if the answer is given to you) to as complex as the answer being in a fairly simple riddle in a nearby book. Another puzzle, if you can call it that, is find-the-switch-that-opens-the-door. Another thing is the traps. There are 7: Swinging blades trap, falling rocks trap, fire trap, spear trap, poison darts trap, spike door trap, and trap doors. When you think of all the work that went into the game, all the miniplots, all the characters, towns, and quests, it's kind of underwhelming how samey all the dungeons are, made worse by how many quests involve sending you into them. I don't think every dungeon needs a unique puzzle or all new traps, only that, considering the number of dungeons in the game, they're in desperate need of a wider variety and more difficult obstacles to challenge the player.
Lastly, combat. Again, Skyrim's is a step up from Oblivion for sure, however once you get to around level 30, things will die in one or two hits, even on the hardest setting. Even dragons, what are supposed to be epic boss battles, become more of a nuisance than a struggle between life and death. This is not necessarily because the player gets too powerful, it's because the AI isn't all that complicated and the combat mechanics allow the players to exploit that. You wait for them to swing, bash, power attack, wash, rinse, repeat. The only problems you'll ever encounter are mages at long range or melee opponents with a shield and a dagger. I never thought I would say this, but this game DESPERATELY needs some sort of miss chance. Enemies die too quickly and it's way too easy to exploit their AI. Enemies that are supposed to be tough feel like a joke when you can stun-lock them with power attacks or, failing that, blast them away with a fus ro dah and hack at them til they're dead. If not a miss chance, some other mechanic that doesn't allow the player to take advantage of staggered enemies. Dragon fights are a special issue. I played Dragon's Dogma, and I thought it was alright overall, but my god, they do dragon fights RIGHT. When you encounter a dragon in that game, it really feels like you're fighting a huge machine of destruction and you are but an ant compared to it. If there is a way to implements Shadow of the Colossus-esque combat into a TES game like it was in DD, it needs to be done.
And there are my two cents. I love Skyrim, and it's up there with my favorite games of all time, but I doubt it will be considered by many to be THE greatest, and in my humble opinion it is the elements I listed above that are the reason for that.

(as long as they dont get their souls svcked out by EA) And I just got Diablo 2 today! (Very late, I know.) It is extremely fun.