Skyrim has a few things that it does better than prior games, but those things are(actually, WERE) done by mods already, extremely easily. For example, someone mentioned the +5 attribute modifiers thing...that was a pretty major problem with oblivion, that, when combined with the way leveling worked in that, game, could become completely gamebreaking.
Unless you installed a 400kb mod called +5 attribute modifiers. At which point the entire problem went away.
Skyrim doesn't have that problem, having had it replaced by the stamina/health/magicka system...but in doing that they completely neglected to realize that some stats would be vastly more useful than others. In an idea sitluation you should be constantly trying to find your ideal balance between the three, but most times when I played(or watching others play) they just put all their points into one skill. One friend of mine always put ALL his points into health, because if you survived you had plenty of time to regenerate stamina or magicka, and on insanity no-death that worked perfectly well for him. That's a symptom of a poorly balanced system.
The quests, I feel, were really hurt by the Radient AI system. In fact, I think the entire game was majorly hurt by that system...I get the feeling that they put a lot of effort into it and felt like they had to use it, evne when the game could have been much more enjoyable without it. Having the same quest each playthrough is still fun as long as the QUEST is good. With Radient AI, NO quest was fun, they were always the same boring thing, over and over, even in your very first playthrough.
The same thing applies to the dungeons. Someone mentioned that they didn't like hand-placed loot, because it means the same thing is there every time. But that's the thing; I already KNOW where everything is, without hand-placed loot. It's in the Loot Chest at the end of the dungeon. What on earth is the point of doing ANY dungeon when I could just sleep for a week and revisit the same easily accessible chest over and over until I get the item I want? Even worse, why even bother doing dungeons when I can just make all the items I need?
Smithing, I feel, was poorly implimented at best. Hit steel with a hammer for long enough and suddenly you're able to forge daedra souls into beaten ebony? How the heck does that work? You should have to do SOMETHING extra to learn how to work each type of metal, either finding a teacher, or melting down weapons and pieces of armor in the hopes of learning the secrets to its construction. Smithing ruined a lot of the mystery of the game for me.
Another thing that really bugged me were the boring equipment modifiers. I guess it was the same as in prior games, but higher level enchantments didn't really become any more useful to me, partially because they took more and more soul gems to keep charged anyway. That's a gripe with all the TES games, really.
Back to quest lines, without the quests that were replaced by the Radient AI, the rest of the guilds felt really bloody empty. Plus, you never had to GO anywhere! Remember back in Oblivion, where just to JOIN the mages guild had you going to every city in Tamriel? Sure, it was a big annoying hassle, but at the same time it gave you a sense of ACCOMPLISHMENT! And even more important, it made the guild feel big, important, a part of the world. In Skyrim you've got one companions hall(where, for the most part, they never seem to do anything) and the Mages College(where again, they never ever seem to do anything. The rest of the towns are empty of them. Which has the side effect of making those TOWNS feel really empty! When the towns in Oblivion had mages guild and fighters guild members walking about, going to taverns, etc, it really made the world feel more real! In skyrim the towns hardly even have temples, let alone guilds. Heck, most don't even have castles, making almost all the towns feel more like Weye did in Oblivion than they way they should be. Dead and Pointless.
The combat in Skyrim is better, but only by a slender margin. They've added dual wielding, slight reactions to being hit and...what else? Combat Cams? (Which are broken, by the way. They've gotten me killed MORE than once, not to mention ENEMY kil cams...)
The dungeons in Skyrim are somewhat better, but that's almost completely mitigated by the fact that they're ALL draugr dungeons. Or caves. But mostly Draugr. The biggest problem is that they all FEEL the same. Cramped, wet, rotting. Even the Dwemer dungeons, which really should have been better, felt little different. I'd say that they really weren't that much of an improvement over Oblivion's dungeons, with the rare exception of a custom-made room with a sunbeam coming in or something.
Another annoying thing is that all you ever run into in Skyrim is bandits. In the forests you get bears and trolls, everywhere else you get Bandits. That's it. No daedra, no spirits, no wraiths, no ghosts...just bandits. Over. And Over. And over. Occasionally wizards, but the thing is, even bandits have their own wizards!
Overall, I don't feel that skyrim improved over Oblivion in any meaningful way. Slight improvements to graphics and combat do not compensate for crappy dragon fights, bad quests and a badly designed everything else.