I was really tired when I wrote that post on game violence last night and didn't hit on everything that I wanted to or expressed myself in a way that I would've liked. I just want to elaborate a few more things.
It isn't the violence in games themselves that makes me uncomfortable, it's how that violence is portrayed, the carelessness to which violence is inserted into games, and the feedback that games give to violent vs nonviolent behavior. Let's look at some examples. Generally, games like Iji and Superbrothers: Sword and Sworcery EP use violence in a conscious and thoughtful way, while the aforementioned Skyrim, Torliight II, and nearly every first-person shooter and action RPG ever created use it in a thoughtless way.
First, let's take a look at Iji. At it's core, the game is a cross between Metroid and System Shock - your character, Iji, jumps through each level with a gun by her side and can upgrade her abilities as she progresses. Although it is possible for the player to shoot their way through the entire game, the player can also run through the game barely firing a single shot, instead simply dodging enemy fire and fleeing from all enemy encounters. What is genius about Iji is that the amount of violence that the player commits alters the protagonist's behavior, changes her personality, and changes the course of the story. For example, the first couple of times that Iji kills someone, she sobs and and exclaims "I'm sorry!", but as the game progresses and she kills more and more and she undergoes a personality change and instead yells "die! die! die!". She grows numb to her actions at first, but she eventually goes mad with bloodlust. Or, in another example, there is a character on the enemy side who, if Iji is pacifistic and effectively harmless, will talk to her, befriend her, and call for a temporary ceasefire. This character proceeds to re-appear in the story from time to time. However, if Iji is violent, then the enemy character will instead simply fire upon her like everyone else and die.
Iji is such a great game not only because it accommodates and rewards both violent and pacifistic play styles, but because it doesn't take violence lightly and seriously takes into consideration the psychological effects that committing violence has on the protagonist. If the violence makes you feel uncomfortable, that's alright: it's supposed to.
Superbrothers: Sword and Sworcery EP serves as another example of an appropriate usage of violence in games, although for very different reasons. Unlike in most violent games in which you engage in hundreds of violent encounters and kill thousands of enemies, there are at most a dozen individual fights in S:S&S EP. This is because each fight serves some narrative purpose in the game - each fight with the wolf builds an adversarial relationship with the character that isn't resolved until the end of the game; each fight to tame a Trigon is necessary for the protagonist, the Scythian, to complete her quest. In contrast, violent encounters in most games exist only for their own sake - the narrative provides an excuse for the violence, instead of the violence supporting the narrative. I would argue that Mass Effect would still tell a fine story if you cut out about 75% of the shooting. In S:S&S EP, the violence is deliberately used as a means to an end, while in many other games violence is carelessly used as an end to itself.
Now, many people who play games do so primarily for the gameplay and not for the story - for those of you who do, having violence as an end in itself and not as a means to advance the story makes sense. In this sense, a game that features completely decontextualized violence - for example, a game in which green pixels shoot red pixels at each other on a black screen - is perfectly fine. However, when the pixels that are shooting and are being shot are replaced with people and when the black screen is replaced with a battlefield, a fortress, or a city, then the game is telling a story, whether the developers take responsibility for it or not. The game is making a statement about violence, and since the violence doesn't deliberatively serve the purpose of telling a story (even though that's what it effectively does), the statement is overlooked by players. There is a sense of the gameplay - the violence - and the story in a game are separate from eachother, but they really aren't. They're both part of the whole. Part of why I think that game developers need to tell better stories through games is because video games are by nature a storytelling medium. Any game that has a setting and characters tells a story, and developers need to take responsibility for the statements that they make as storytellers.