After close scrutiny there are some problems that arise with Skyrim...

First off the intro...
It's pretty subjective topic but I have to give it off to Extra Credits on this one.
http://www.penny-arcade.com/patv/episode/skyrims-opening

Second, the dwemer ruins...
That place is easily the most obvious representation of copy and paste dungeons.
The place gets to the point of fatigue it's just that you don't want to be there any longer. Instead of being mystified by it's history. I felt most of the time that I was traversing the same terrain over and over again with little variety that it felt like a cheap way to extend game time.

Third, bugs, bugs, bugs...
Bethesda is quite synonymous with the word glitch or bugs attached to their title. Past games evidence this a lot. And I'm sure there's quite a lot of you that differed from your gaming experience because of a snag in the game which prevented you from questing further or was literally locked with a quest objective. Quest items after completing a quest would clutter your inventory, misc quest pointing to the ground. Just a bloody mess. For one to have a dedicated save file of 200 hours and up and to find this stuck to their game file. Not even patches can fix something that's been broken. Time to start another game and experience that bug again. If your on pc good for you. If on 360 well crap. If on PS3, better get a pc version or 360.
Perhaps Bethesda should examine different types of permutation gamers might do when exploring Skyrim. Bioware nails it, even there are many arching story plots it stays consistant.

Fourth, Interface...
Interfaces are dependent on the system. The problem I had the most was the map. The map was terrible imo in contrast to Oblivion. I found that the weather in Skyrim interrupted the labels on the map. PC's menu was that of the xbox 360. It took some fan mods to fix it to represent the pc and keep the skyrim aesthetic.

Fifth, respawning items in dungeons....
I can understand respawning enemies, but respawning items. Makes no sense if I cleared a dungeon. Collected every item including dishes and to come back to find it return. in the same exact place. Totally breaks immersion. It's like playing a fallout game going into a convenience store. collecting food, wait a couple of days and someone restocked. I thought this was post apocalyptic.

Sixth, NPC's know who you are even when you're wearing a mask.
Seems pretty similar to Oblivion's all seeing guards. Perhaps a system that show if masks hide your identity or not. At least Obsidian put effort making this realized in Fallout New Vegas.

Seventh, fresh fruits in old dingy dungeons...
Yeah I'm going there, at least in Dragon's Dogma there was rotten fruit. Here's hoping Dragonborn DLC or future DLC adds new items in dungeons. Rotten Apple, etc...

Eight, items serving no purpose...
Lanterns, really you can't light a lantern?

Nine, drugs have no negative feedback.
In Oblivion Skooma drained your intelligence. In Fallout 3 you can get addicted, screen gets blurry, visual cues feedback, etc. In Skyrim, nothing no visual distortion, nothing. Disappointing.

Tenth, Skyrim, not as open as you may think.
You can't make your child a vampire or werewolf. You can't remarry if your spouse dies. You are still constricted.

Eleven, why no footprints in the snow...
Self explanatory. If legend of Zelda Windwaker can do it so can Skyrim! Oh wait, that's only on pc mods.

Twelve, the houses just svck.
I look at Hearthfire and I weep. Remember in Oblivion. You bought a house and there would be secrets. A hidden wall. A tomb to stash your gems. In fallout 3 you can change themes.
In Hearthfire you are restricted to a house that simply screams out HOARDER. Seriously Bethesda what are you promoting by having so many bloody sacks lying around. The design is fixed and horrible. I've seen great mods by fans that seem more appetizing. Heck I would pay money for those fan mods to hit the xbox 360 console.

Thirteen, story isn't memorable.
In Oblivion there would be twists in the story. I remember you had to fetch a ring in a well only to realize that the ring you picked up weighs a lot and if you don't get rid of it in your inventory you would drown. Dark Brotherhood missions like Who dunnit was amazing as it changes up the variety of the mission in context. Mages vs necromancers. Here it seems that the story is forgettable and plays towards that casual audience. I guess that's just nostalgia speaking but it doesn't capture the variety of mission types. In the end Skyrim mostly becomes a go here, kill that, retrieve this, etc...

Fourteen, radiant quests get boring quick.
Here's looking at the Thieves guild quests given by Vex. So boring that there's no challenge. Simply becomes a bloody chore. There are other ways to rake in money by playing the game regularly and looting bodies. Radiant Quests in the end became a chore and quite tedious if you want to become the Thieves Guild leader.

Fifteen, don't have gamers feel regret when playing your game.
Let's be honest there are people who can't recognize if an item is unique and one of a kind. Perhaps a marker indicating if something is unique and should be sotred rather than sold. Sell something, play hundreds of hours, realize the item is missing. Player feels regret. You don't want that in a game. I feel bad when I look at my past quests and I see failed in that mission. Then comes to the point of redoing it. I hate seeing that in my list of history. There's no benefit from failing a quest only that a red x appears there.

Sixteen, hard to showcase your stuff.
In Skyrim it's quite difficult to showcase your items. I kinda wish I can put all my dragon claws (ruby claw, sapphire claw, emerald, etc in placeholders and put it in my home. It would be great to have my priest masks on display. Bethesda lacks these things. In the end if your pc you can easily get it.

Seventeen, if fans want it give it to them.
So far I know of one developer that listens to the fans and delivers. That's Gearbox. Fans want this in their DLC. They deliver. Bethesda listen to your fans. If gamers want this, give it to them (if within reason). No point creating fan expectations in these forums as they dream up awesome and interesting things only to be let down that they won't come into existence in the retail game. Console gamers are stuck with what Bethesda intended. PC gamers have flexibility but are more prone to piracy. Console gamers spend a lot on things like DLc so deliver these things to them.