Basically, a question for gamers everywhere of the Elder Scrolls about what they want from the next game in terms of the ability to do what they want. There's a lot of freedom in all of the games compared to other titles but part of the problem is this often shoots the narrative in the foot.
Let's take the Companions quest. One of the more controversial stories in Skyrim for freedom. In order to advance in the story, you need to become a werewolf. Likewise, a lot of players wanted to team up with the Silver Hand to slaughter the Companions. This would have added to their personal RPG experience that they're really hateful of "monsters."
On the other hand, the storyline with Kodlak Whitemane is that he is a figure trapped by a curse and needs to escape it. It also affects your relationship with the character that you, yourself, are trapped by the curse (or feel liberated by it). A limited amount of railroading was necessary to maximize the effectiveness of the tale.
The Dark Brotherhood quest gives you the option of slaughtering them completely, however, this is kind of cutting the branches of a significant amount of content. Is this the kind of freedom we want? The option to keep to our roleplay but completely shoot down the artists' vision?
"Dawnguard" remains the most interesting of the tales, IMHO, because it allows you a maximum amount of freedom to choose between the factions and what they accomplish. Even so, a major part of the tale was railroaded because the character of Serena is so central to it. If you could kill her in the first place, well, the story wouldn't be nearly as entertaining.
There's also the fact that developers have only an X amount of time to develop things. The more they develop storylines with multiple choices, the less time they have to develop other stories without them. Part of this may be why the villain in Skyrim is Alduin followed by the Thalmor.
No rational being supports the end of the world so the Dovahkiim will support stopping both no matter what their ethical stance.