So there's a reason they aren't on my top 10. And it's not because Persona 4 came out in 2008.
(Persona 4 and Catherine spoilers, naturally.)

Persona 4 does something most games don't even consider. It actually introduces a character who actually represents a social issue Atlus generally struggles with, Gender identity. 

Now let's set aside a quiet moment at the start to clarify my position here. You might want to point out that I may have an empathy bias, since I’m gender dysphoric myself. My perspective on this kind of topic is hardly impartial, and this possibly a little more personal than I ever expected one of these blog posts to get.

Now the first thing anybody else, who took the social link to it's conclusion, would be probably be quick to point out is that the overall issue Naoto's arc addresses is sexism and yes, in the ontext of Japan circa 2008, that was still something games needed to handle better. I could sit around and take issue with how it handles empowering her as a female post-arc and in the stories after the events of the game, but that's sort of besides the point of this article. Though if you can name games and characters that explore the topic better, feel free to suggest them.

Sexism, suicide, and on rare occasions, sexuality have been topics game have often tip-toed around and to some extent still do. (Remember the outcry against SWTOR for being about "sodomising your crew"?) So with even these concepts that in other media are often eager to explore, it's understandable that games haven't explored less visible topics or stories like gender identity more. I'll give Atlus credit, they have some social links that do good things like actually having a male character grappling with bisexuality. But his struggle also ties into Naoto adding another source of confusion, and the ultimate resolution of both his and Naoto's are a quite typically Japanese. I'll paste in a quote from an old gamasutra article.

"The Japanese see homosexuality as a lifestyle choice, very different from the actual homosexual activity," explains Dr. Antonia Levi, author of Samurai from Outer Space: Understanding Japanese Animation. 

"There is an understanding that you can play with fantasies that you might not want to live out in your normal life," Levi says. "Americans see things in very black and white -- you're either gay, or you're not. The Japanese are more comfortable with the concept of being gay and not being gay at the same time. In this case, it makes sense that, in the end, the game is not telling you what to think about Kanji or even if he is gay."

To put it more plainly, it's more typical of them to regard these sort of things as separate from your public life, but to actually come out as gay or transsexual is very different to simply having a "second life", it's seen as being confrontational with normal life. When you consider this, the way that Atlus bring their social links back around starts to make a lot more sense.

That's why Naoto's social link instils such discomfort in me. In the main story, it's introduced with Naoto openly acting and operating as the detective prince, when you encounter Naoto's shadow, the game starts to raise the topic of gender identity as a symptom of feeling confined by the idea of embracing a more "traditional" role. To Atlus, or to a Japanese player, dressing like a boy is Naoto acting against societal norms, so it only makes sense that you're basically put in a position of being the one that steers her towards dressing an acting more "acceptably" in order to facilitate and uncomfortably controlling romantic relationship. It trivializes the struggle with one's gender as just something to be played at in the greater context of Sexism.

It sort of all resolves in a very Japanese way, and this is where Atlus' other game of 2012, Catherine starts to address transsexualism more directly than a footnote in P4 or outright comedy in Persona 2 or with Transwomen as deceptive sexual predators in Persona 3.

After avoiding the topic, it's hard to see how Atlus could go from having transsgender topics as (rather offensive) blips to as problematic a character as Erica Anderson. Now, I'm going to assume you're familiar with the context of Catherine, if you're not Catherine tells the tale of Vincent, who begins having nightmares after he cheats on his longtime girlfriend. Every man who has these nightmares winds up dead and only men are able to have them. Later in the game, these dreams are revealed to be a divine punishment for men who keep partners who want children from having them.

The gameplay does little to tell players that Erica is in fact transgender, but when it's finally stated explicitly in the "true ending", it makes the hints dropped by the characters that knew look very different in retrospect. In the same moment you're explicitly told that she's transgender, she's outed as "Eric" by Toby and earlier on in the game he expresses regret at having slept with her having not known, and complaining that the sex "was weird" despite her having undergone reassignment surgery in high school.

Throughout Vincent’s time in the game’s bar, he and his friends are amicable to Erica but also say rather disparaging things about her femininity, often commenting that she's not "a proper woman". The group of men seems to put up with Erica rather than appreciate her friendship, and is vaguely trying to steer away the youngest member, naïve Toby, from pursuing his attraction to her, eventually writing their efforts off, saying "everyone's got their own problems to deal with.".

The second hint comes after Toby and Erica sleep together when Erica shares that she is starting to have the nightmares, which only men are supposed to be having, however it is easy to overlook this, as it appears whoever goes to the bar has these dreams until it's later stated that only men will suffer the nightmares.

It might be tempting to say that because the only real overt transphobia comes from the main villain, who happens to be her employer, and that Atlus is taking a favorable position on transgender representation in Catherine. However the game has characters largely either being annoyed by her or talking down about her, and frames her sexual encounter with Toby as a malicious act on her part as he expresses regret losing his virginity to her, and discomfort with the idea that being able to sleep with a transwoman   should lead to a questioning of his sexuality by extension. Malicious enough that she's considered to be on the same level as many other more lecherous male characters, simply because she's biologically incapable of bearing children for Toby rather than actively or intentionally denying him a bloodline.

There’s the unfortunate fact that Erica having these dreams means that she’s on the receiving end of divine punishment for being closeted to a guy she slept with. Given the violence and transphobia that trans people become the target of when not closeted, the very idea that a trans woman deserves to be punished for keeping this secret where Atlus writes stories that actively encourage keeping public and personal life separate is rather ignorant.

Her friends don’t show any support and have extremely little respect for her identity as a woman; as well, her boss is constantly hitting on her, despite that he was the one judging her as being as bad as every other male condemned to the dreams. Erica herself is a great character with relatable dialogue for the most part, but the politics surrounding her story doesn’t provide any optimism for trans-folk and ultimately these stories serve to offer more in the way of doubt than hope.