Art in general and games in particular have an uncomfortable relationship with discomfort. People don’t like being made uncomfortable– at least, not when it’s called by that name. Really, though, discomfort tends to come hand-in-hand with novelty. Anything that’s new and unfamiliar makes people uncomfortable, if only slightly, until they have a chance to get used to it and come to understand it. And, following that thread, novelty comes along with learning: You’re only really learning if you’re processing new information, even if it’s just an extra tiny facet of something you knew, each facet contributes something to the whole. And, as Raph Koster argues convincingly in his book A Theory of Fun, the fundamental activity that makes most games fun is learning.
Thus, to some degree at least, games are designed to make us uncomfortable.
This isn’t really that counter-intuitive. Much game design literature talks about how to challenge the player without frustrating them– largely a matter of the degree of challenge and how it is presented. It is considered desirable, though, to try to minimize frustration, to minimize discomfort, in particular that frustration and discomfort which isn’t a direct result of the challenges the game proffers– or, more precisely, the challenges the designer meant for it to proffer.
Games tend to try to minimize the discomfort for new players by establishing a common language of genre conventions: Once one gets used to the conventions of a given genre, it’s usually not too difficult to get started playing another game in the same or a similar genre. However, these conventions drift quite a bit over time: while playing Modern Warfare 8 will presumably allow one to transition fairly easily into Battlefield 13 or War Soldier Battle Man 6, trying to transition from Quake to Counterstrike is quite a bit more difficult.

None of this is intrinsically bad or good, but it can cause as many problems as it can solve. When the language of a genre becomes too well established, you end up closing off any space for innovation within that genre– that is to say, the attempt to make an experience which is immediately accessible to anyone familiar with a given genre, when taken to its extreme, is in effect an attempt to make a game completely disposable and uninteresting. This may seem obvious, but it supports my earlier point that aspects which make players uncomfortable are not something one can hope to easily trim away to improve a game. Often, the uncomfortable parts of an experience are those closest to its core, and when we trim those away we have nothing left.
There are other traps as well, silent and insidious. As you reduce the discomfort of your game to the minimal level you can achieve, targeting for fans of the genre, you may be making your game even more esoteric and bizarre by the standards of those who are not aficionados of that genre. The fans will continue to clamor for deeper and more intricate simulations to push at their understanding of your game and force them to learn, but this results in a sheer wall of information for a new audience– conversely, if you had instead decided to expand the topic of your game into some intuitively connected area, or to take a new approach to the same material, you could have provided your core audience with new challenges to explore while, at the same time, not created an insurmountable information wall to newcomers. This trend, towards more in-depth simulation at the cost of accessibility, has repeated itself over and over in the history of gaming, and tends to signal the death of a genre when it does.
As artists, as humans, discomfort is our guiding force. Discomfort is what tells us where the conflict at the heart of the story lies– or where in our own heart, in our own story, lies. Discomfort, discontent, unhappiness, these are not our enemies: Without them we would never know anything was wrong.