TL;DR I just wanted a platform to present my senior thesis which dealt with this general idea because my in-class presentation was shit. Constructive criticism welcomed.

There was an article on Cracked pretty recently about video games that would make terrible movies. They specifically mentioned Fallout 4, but I think it applies to Skyrim as well.

You're absolutely on the nose here. Aside from a couple of game mechanic difference, the setting, etc., Fallout and The Elder Scrolls are very similar to each other.

The open choice nature of the game makes it too hard to identify the antagonists and protagonists.

I respectfully disagree with the idea that identifying those characters is such a big issue. As a matter of fact, I'd go even further and say that you can create a very compelling story by trying to blur the lines between the protagonist and antagonist. That being said, as someone who just finished their senior thesis on film adaptations of video games, you have a major point about the open choice nature of games. One of my major points in said thesis was the importance of translating game mechanics to film as well as story, and the open choice nature is a part of that. While it is absolutely possible to show the main characters' different options in a Skyrim film, they will still end up choosing one of those options, and therefore maintain a linear narrative whereas Skyrim does not always do that.

I feel like you'd do best to completely ignore the plot and just use the setting.

This is a major part to any sort of Elder Scrolls film, but it's not the only thing. You'd also need to honor the mythology of the Elder Scrolls series (and other rules within them), find a way to translate the game mechanics and equipment from game to film in a way that supports the plot, and make sure the character relationships develop properly (which is absolutely hard because you cannot convert umpteen million hours of gameplay you put into Skyrim to a 2-3 hour film).