Skyrim is a huge and uneven game, and I will be discussing many of its high points. In the spirit of getting the bad news out first, however, I want to discuss the game's secondary quest, concerning the civil war between the Imperial Legion and the Stormcloaks led by Jarl Ulfric of Windhelm. There is much to admire in the way this quest is set up, but as a world element and gameplay series it falls short in several respects. Primarily, although the quest successfully conveys the social importance of the conflict and the philosophical differences between the sides, it fails to make the war a vibrant part of the setting or provide a feel for the military differences between the two armies. More importantly, because the quest mostly fails to integrate with the game's other plotlines, it feels overly inflexible and misses some great opportunities.
Skyrim sets the stage for the civil war questline immediately, beginning with the player-character riding in a cart along with Ulfric Stormcloak towards an execution to be carried out by the Imperial military governor, Tullius. Once a dragon crashes the beheading party, the player can choose to escape the city with a Stormcloak or a Legionnaire. This is a non-binding decision, but for those who play the game twice, it holds the rewarding revelation that the apparent relationship between Hadvar and Ralof is due to their living in Riverwood. Shamus Young has a post detailing the other strengths of this opening, so I won't belabor the point.
What's disappointing here is that the civil war subsequently drops almost entirely off the radar, existing mostly in dialogue. What the characters say is often clever and convincing - I especially liked the dueling, equivalent propaganda songs - but because the war isn't truly built into the world the sense of conflict is lacking. The player may encounter an occasional patrol of soldiers, but there's no evidence of armies moving into position or striving against each other. The image below originates from GameBanshee, and I've modified it to show where the supposed Imperial (red) and Stormcloak (blue) forts are positioned. Until you get fairly late in the quest, however, not one of these has any soldiers in it: they're instead occupied by bandits and rogue mages.
The conflict only seems real at Shor's Watchtower, which has a bunch of dead Riften Guards (not Stormcloak soldiers!) in it, and a written message stating that Imperials are marching on the position. This is also not a success, because it doesn't make any sense. The Watchtower guards a road between the Rift and Eastmarch, two Stormcloak territories. As such, there's almost no strategic value in a hit-and-run attack on the place, though there would be a substantial advantage (and an excellent local plot) if the Imperial Legion were to, say, take it over and disguise themselves as Stormcloaks so they can intercept messages or interfere with commerce.
The most tangible display of the war comes after the matter has concluded, at which points the forts that you have conquered remain staffed with soldiers from your side. Enemy camps will still be full of soldiers, however, and the forts that allegedly belonged to your side from the beginning will still be occupied by whatever enemies held them at the start of the game. Even the fort you take over single-handedly to prove your worth to the Empire will be back in the hands of bandits!
This is also a missed opportunity, as it could have been used to draw a contrast between the opposing sides. The Empire could go back to being "nice and lazy", as the doomed Lokir describes them at the beginning of the game, letting the forts be reoccupied. Ulfric, who needs to maintain control over the holds in order to ensure that he is selected as High King, would be more likely to leave his troops in place as a way of demonstrating power.
The problems the game has dealing with the war before and after the main quest, however, pale in comparison to the way it handles the player during the quest itself. Skyrim does an admirable job of offering two alternatives of roughly equal appeal. The Stormcloaks are initially the most sympathetic because they're going to get killed alongside you, and Ulfric shares your ability. However, the Stormcloaks turn out to be big, fat racists. The Imperials seem to make more sense for a character who wants to preserve humanity from domination by the Thalmor elves, but they're fairly racist themselves. Moreover, they have a not-unwilling hand in the religious oppression that the Thalmor impose on Skyrim.
Unfortunately, these options don't quite encompass all the motivations a player can come to the quest with. Consider a player who has decided to be pro-Thalmor (the game makes this extremely difficult at every turn). The best outcome for the Thalmor is that the civil war continues indefinitely, but there's no way the player can actively ensure this. Alternately, any player who pays attention to the world's lore will note that the Emperors used to be Dragonborn. Since the game makes quite a big deal of the fact that the player's character is Dragonborn himself, the player might reasonably come to the conclusion that he ought to be Emperor. Again, there's no option for the player to work towards this goal.
What can the player do? Well, the campaigns mirror each other quite closely. The player performs a feat to convince one side or the other to take him in, then goes dungeon-delving to retrieve a crown of symbolic importance, which is never worn or mentioned afterwards. Then there is a battle for Whiterun. The player defends it if Imperial, and attacks it if siding with the Stormcloaks. Having to depose Jarl Balgruuf is a serious emotional cost on the Stormcloak side, and a very well-made choice. It would have been nice to have some slim chance of talking him into supporting Ulfric, however, or to make Balgruuf's death, rather than banishment, a consequence of the Stormcloak choice.
After Whiterun, the player goes through a series of small quests that all culminate with taking over the primary fort of each given region, whether these forts are in a strategically useful position or not. Finally, either Solitude or Windhelm is conquered, depending on whether one is playing Stormcloak or Imperial, and either Tullius or Ulfric is killed.
That the campaigns are precise mirrors of each other might have saved time, but it's a missed opportunity. The two sides play identically even though the armies have very different natures and motivations that could have been accentuated through gameplay. The Imperial Legion is a large force operating as a massed army in an essentially foreign land. As such, its primary challenge is projecting power, and the goals of its actions should be to take and hold forts on key roads and waterways, and defend its supply lines. Specifically, though, it needs to thrust towards Windhelm and take out Ulfric, without whom the rebellion will probably collapse.
Most of the action in the existing quest is a good fit for the Imperial strategy, though there is no reason for them to take Winterhold or Fort Hraggstad, nor to bother with the crown. The player should have instead been instructed to take over Robber's Gorge (which is actually a small wooden fort), fend off Stormcloak attacks on interior supply lines (the Reach would have been a good spot), or retake Helgen from the bandits that have moved in, to enable a flanking attack on the Rift. Also, the existence of the Imperial camps, with the possible exception of the one in the Rift, doesn't really fit the Legion. These should have been removed, and the player given his orders from the point of central authority in Solitude, to emphasize the nature and intrinsic vulnerability of Imperial operations.
In contrast, the Stormcloaks are an indigenous army fighting a stronger and better-supplied force. They are also traditionalists who are very impressed by symbols and signs of strength an valor, which is why Ulfric ought to wear the Jagged Crown. In the context of this conflict, Ulfric's challenge will be in concentrating his power. He doesn't need to conquer every territory; he only needs to make it difficult enough for the Legion to operate that they withdraw. Once they are gone and he has assured himself a majority vote in the moot, he will attain his goal of becoming High King.
Here again, the choice of Whiterun as a turning point in the war is correct, not so much because Whiterun is important to Ulfric per se as because holding it gives him the one vote he needs and makes Imperial operations much more difficult. As such, most of the Stormcloak campaign should have focused on taking that city. For the Stormcloaks this could be a multi-phase quest, with the player taking part in small assaults on Valtheim Towers and Whitewatch Tower to allow Ulfric's army to move freely. Then the player should take Fort Greenwall (potentially all by himself) to interfere with Imperial movements and cut off reinforcements, before then assaulting Whiterun.
There's no reason for Ulfric to move on Falkreath, although the game could integrate the Dark Brotherhood questline here (if active) by assassinating the young Jarl and replacing him with his deposed pro-Stormcloak predecessor. Similarly, there is no need to conquer Hjaalmarch (where Morthal is located), and that campaign could be replaced by an assault on Dragon Bridge.
Markarth's territory, the Reach, is more complicated. It's an important source of supplies for the Imperials, and more importantly it's the place where the Stormcloak rebellion began, when Ulfric was imprisoned for worshipping Talos despite the promises of the local Jarl. The Forsworn who inhabit many sites in the Reach as part of their own guerilla war are also opposed to Ulfric. Markarth itself is pretty impregnable, but the tough geography of the Reach is ideal territory for Stormcloak guerilla operations.
Here again external questlines could be entangled. Ulfric could send the player to spring the Forsworn's king from his jail (as part of an existing quest in Markarth), giving him the Jarldom of the Reach in exchange for a promise to support Ulfric's case at the moot. Or, the player could be sent to retrieve Red Eagle's sword and give it to Ulfric, making him the symbolic leader of the Forsworn. This alternative would also serve to build the image of the Stormcloaks as traditionalists.
It would have been easy to choose a series of quests that highlighted the differences between the two sides. Instead a restrictive and lazy sort of mirror-image strategy was employed. Even in a single playthrough the civil war questline rapidly becomes dull and repetitive, and while the differences between the two sides are easy to describe, they exist almost entirely in dialogue rather than in gameplay. The resulting quest is not bad outright, but it is much shallower and less interesting than it could have been.