Okay so.

Obviously, Yu has some gender non conforming in-text elements. He does 'traditionally feminine' things. And I love headcanoning him as a housewife type, eager to please (his husband, preferably Adachi, but we could go with other men too). And I especially love him as a bit coy and coquettish, doubly so when he's the bottom. Playing up his youth and innocence, if that fits for the setting. That said, I see him as such a Male Character that it takes me a bit to hop into fem!Yu fic and headcanons. I view him as a gender nonconforming man, at the end of the day. (And I do like headcanoning him as ftm trans, too.) He's so comfortable in his masculinity that he doesn't feel the need to keep up with over displays of masculinity and especially doesn't play into toxic masculinity. He is passive without being just responsive (though this is arguably more about the gameplay of P4 than explicitly written). Also, he slots into the Dojima family as both an older brother to Nanako and a caretaker that can handle the emotional fluctuations in the house...which it seems Chisato was largely responsible for before her passing.

While I see Yu as solidly rooted in his masculinity/maleness, I see Adachi as constantly trying to prove his masculinity to himself and others. His murders are so obviously deeply rooted in....so many issues, one of which is heavily tied to masculinity and expectations of men and their sexuality. (Hence why I'm not as bothered by the 'incel' stuff as others often are. I don't tend to focus on the 'incel' aspects of his character for a few reasons, but i think it's a fair accusation when reading the English text.) He oozes comphet. A lot of his anger and frustration can be attributed to his professional failure, of course, and I appreciate explorations of that! But I really like exploring Adachi as a more queer character who doesn't have the language or even cognitive groundwork to understand what he's feeling and why. There's something about his manipulativeness and underhandedness that I think can be seen as feminine, in a way. I can only speak from a Western perspective, of course, but more 'subtle' uses of power are often associated with women. Adachi is passive in a different way than Yu; Adachi waits for the proper moment to strike or twist the situation to his benefit. That sort of behavior isn't associated with masculinity and male power, at least in Western thought.

(Whereas we can read Yu as only utilizing his power/authority in appropriate instances, but he is very firm and aggressive when needed. Adachi gets pushed into lashing out; he doesn't do his great big villain speech without the Team confronting him into a corner.)

I also see Adachi as being more fluid/mutable, a trait we often see assigned to femininity, than Yu. Of course Yu has different faces for his various social links, but I think he maintains a more rooted sense of self compared to, say, P5's Akira. (Who I view as a liar, at heart. I love him.)

Going into solid AU/headcanon territory, I love tinkering with the idea of Adachi having more/primarily female friends. Whether it's Izanami as a human (or human friendly god), other characters in the canon, or OCs...I think Adachi would be a catty bitch and get along with other secretly catty bitches. (AUs where Adachi and Saki interact and are friends are like....my life.......) I also love the thought of him realizing he has more in common with women in how he interacts/manipulates the world than with the men around him.

When it comes to the both of them, I really like thinking about how they are the ones 'acted upon' by Izanami (vs the ones initiating). But I love love love Izanami, so.

Anyway. That's basically why I like writing them as men (trans or cis). I enjoy other headcanons for them and have some WIPs for fem!Shuada, but I think that changing their genders really changes their dynamic and how they interact with the world, so I try to consider that when writing.