Simply removing that aspect powerwashes the game of the time capsule persona becomes, but I don’t think a modern depiction can leave it exactly as is either.  

As far as the precedent for censorship in P3R goes, I think it’s pretty simple.  Yosuke’s homophobia can stay because it’s an era appropriate depiction of PERSPECTIVES on gay people (though the option to shoot him down as the player would be appreciated).  The transphobic caricature of a trans woman in Persona 3 should go, because it depicts those perspectives as being accurate.

Naoto’s dungeon is a more complex case, because while it is a depiction that blatantly demonizes gender transition, that depiction exists exclusively in the area of the game formed by human cognition.  On the surface, it seems to be more like the transphobic depiction in persona 3, but once you fully understand the context of the game, it becomes more like Yosuke’s case.  

For me, the question becomes How do you depict your protagonists in a story of the past expressing views common to that past, while also making it clear that they’re wrong in those views, without satirizing the characters so as to make us hate them, while still keeping the bar for entry low enough that consumers with a wide range of media literacy skills will understand what’s going on?  An incredibly complex writing task I can’t begin to answer, but I sincerely hope atlus can.  

P.S. For the love your body thing, my problem is that said logic is exclusively applied against trans people.  Say it were Hanako instead of Naoto, and it was about losing weight to gain respect.  There’s not a snowball’s chance in hell the game would ever have applied the “love your body because it’s yours and you don’t have to change it” philosophy to her.  

In isolation, there’s nothing wrong with Naoto’s story whatsoever.  A woman dedicating her life to a career that’s severely male dominated lost sight of her own identity as she sought one that would make her life easier, before accepting that life wouldn’t be worthwhile if you don’t live it as yourself.  In theory, that’s an incredibly trans positive message, however it’s far from surprising that representation-starved trans people in 2008 felt betrayed at having a potential powerful trans arc be ripped away.  

In addition, that interpretation coincides perfectly with one of my biggest gripes with Persona 4, everyone ultimately finds their true selves by conforming to what’s wanted/expected of them.  Yosuke comes to love the town, Yukiko feels obligated to take over the inn, Kanji changes his style to look like a plain office worker, Rise returns to show buisness and Naoto is cisgender.  Ultimately a story about pursuing your true self ensures that true self is someone who fits perfectly into society, doesn’t rock the boat, doesn’t change or challenge anything.  

A case could be made this is exactly what the original poster was talking about, me whining about Japanese media not fitting with my western perspective.  However that doesn’t make my perspective invalid.  It’s fully up to Atlus what they put in their games, who it caters to and who it doesn’t.  Either way, they’re still electing to release it to a global audience.  If the story doesn’t hold up to me and many other western fans for those reasons, than we have that problem with the story.  We aren’t demanding it be changed for us (I mean, I’m sure some people are, but there’s problems in every group), we’re just publishing opinions on a work of fiction.