This is definitely an interesting topic, and one that I’ve tried to consider a great deal. I’m definitely curious to know how more people feel about this.
I should disclaim that, being male and cis, I’m not personally disadvantaged by most of the factors people have been talking about in this thread. I am gay, though, so I can explain how prejudice in games personally affects me. I hope that these themes are important and applicable to the question of whether or not to include prejudice.
My inclination would be that there is value in having both stories/games that deal with themes of discrimination, and ones in which it isn’t a factor at all. Discrimination can be very powerful and very moving to read about, and is such an important part of experience that it is worth writing about and worth reading about. At the same time, it can get very tiring when that’s all there is to read. It’s incredibly affirming when I can read or play a gay character in a story that isn’t about being gay, doing all the things straight characters always do. I don’t know if people who aren’t marginalized always understand how confining it can feel to look around stories and constantly feel like you don’t belong, and that when you do, it’s only for a moral about prejudice.
So basically what I’m saying is that they both have a place. Being such a major part of experience, I wouldn’t want to see prejudice being always ignored, and I really value it when works of media can explore it deeply. But I also want to see works that aren’t about it, and still give the characters the same opportunities. That doesn’t mean a story can’t still be gritty, if desired. And prejudice themes require that the author give them full respect, and not merely exploit them, or throw them in without consideration.
It also really depends a lot on the story and setting. (And tone, for that matter.) I’ll just give a couple examples from two of my favorite CoGs, in which, despite how much I enjoy and esteem them, I would rather they handled things differently. Here I’m just talking about gay characters, because that was where I personally felt an impact.
In one direction was Hollywood Visionary, which takes place in the 1950s. For the most part, the characters around seem like people who would reasonably make sense as more tolerant than typical, and the romantic stuff is not too public, anyway. However, there is a very bigoted man. If you look at the code, you’ll see a short bit of writing in which he would have been homophobic to a main character involved in a gay romance, and another character would immediately thereafter comfort the main character. But this bit of writing is hidden by the *comment command, and would never be visible when actually playing the game. I found it very touching; the inclusion of such a strongly supportive character in the face of adversity felt more valuable to me than the version we got, which papers over this. There is also a character who, if they are the same gender as the main character, may express having once been married to someone also of the same gender, which also feels like it doesn’t acknowledge the dynamics of the '50s. (I mean, sure, one of them could’ve been trans, or it could’ve been a marriage that wasn’t done by law, but they considered it marriage nonetheless… but it’s still an example of one of the places where some acknowledgement of being gay would’ve been nice.) In general, despite the wonderful inclusiveness of the game, and its versatile gender-related options, it feels like something is missing from the experience of a gay person in the '50s.
Now, on the completely opposite side of the fence, there’s just a single little discrepancy in Sixth Grade Detective, which otherwise reads pretty much the same no matter the sexual orientation.
At one point, when the main character meets Darren, the uncle of a potential romance, A.J. (whose gender the player can select), this uncle can tease them by asking if the main character is A.J.'s boyfriend/girlfriend, which gets A.J. all embarrassed. But this only happens if the main character and A.J. are girl/boy or boy/girl.
When I saw this in the code, I felt like a little bit of cuteness had been stolen from me. Sure, I can see a justification, that Darren would make the same heteronormative assumption that many people make, but I don’t care. It’s a fluffy story, there’s no exploration of discrimination, which would be jarring with the story’s tone in any case, I get a chance to have a gay kid in a story that has absolutely nothing to do with him being gay, but allows him to express it in as natural a fashion as heterosexual characters usually get to… and I want my gay kid to get an affectionate tease just the same as any straight kid.
So my point from these two examples is that context, setting, and tone are key, and the way the author handles it makes a big difference. There is a place and a time to address prejudicial themes, and there is a place and a time to let characters experience the same stories without being weighed down by the same baggage they have to deal with in life.
(We also shouldn’t assume that our history’s prejudices are the only way these prejudices could’ve developed, and that discrimination in games would work the same way we’re used to. It could be interesting indeed to explore a setting that developed in a distinct and different way.)