There don't have to be drastic changes in the game world to make some visible changes according to the player's actions...
The dragons flying around Skyrim during as long as the main quest is active should honestly be twice as many as they are now, and much more agressive towards towns and villages. After the main quest is over, it only makes sense they'd become much rarer, like half as many as now, and not hostile...
Being a member of the dark brotherhood should have an impact on the other ppl, something like a special intimidation option similar to the bribe thieves guild members get.
Finishing the civil war questline should have much more profound results than simply different guard apparel and a couple extra NPC lines, period. No need for something drastic - just adding A LOT more NPC lines and making it so that I automatically get some status similar to that of a thane across all Skyrim - since I am the one who was the right hand of Tullius/Ulfric in the war...
All these can be accomplished with minimal effort and consist mostly of more dialogue variety and options... and no, don't tell me they can't put resousres into such trivial things, because they did put special dialogue for things like having Azura's Star and putting perks into speech, WHICH IS THE DEFINITION OF TRIVIAL! (actually, it's the definition of stupid, because the NPCs have no way of knowing all these stuff in the first place...)
Oh, and we do certainly need a proper faction reputation system as well... we kinda have it with orc tribes and a couple other things, it should have been for sure been expanded to the Forsworn, Vigil of Stendar, Silver Hand and Vampires...
And one final thing: in a game that took 3 years to finish, that has sophisticated graphics, voice acting, LINEAR quests (yes, they're many but they're all linear, apart from some small side quests which shouldn't have any effect in the world anyway) and a sizable budget, it's not the player's role to tell the story. It's the game's. The player has to CRAFT it, and the game should translate the actions into effects. Again, NOT ALL OF THEM - yeah, the world should still be the same after I help an old lady in some faraway hut in the forest or kill a couple travelers in the tundra, but when I save the [censored] world from a homisidal phsychopath immortal dragon, the game HAS TO SHOW SOME DEFINITE SIGNS THAT SOMETHING CHANGED IN THE WORLD!!!
Bottomline: it's not minecraft. I expect the game to be able to do some basic things by itself. I expect a semi-dynamic world, that responds
accordingly to the big things I do, and not to stupid things like putting a perk to sneak and finishing some stupid sidequest...