In persona 5's case, it's less of a lack of representation and more of a lack of ambition in what it set out to do.
When early info on P5 came out, about how the game was about people who were affected by society, I was expecting a game that pulled back the curtains on issues in real Japan, things like homelessness, drug addiction, race relations, etc. I was hoping for a game that got down and dirty and honest with these sorts of things. It'd be shocking and real, the kind of thematic step-up that would make Persona a real powerhouse.
And while persona 5 does have things like that (societal stigma against criminals, false conviction, abuse of power, abuse of women, etc), it's ultimately a very clean game. It challenges the player, broadly, to go against authority where the greater good is concerned. And that's all well and good, fight the man, fuck the cops, etc
But it's still ultimately just a power fantasy for the Everyman player. How you, the player, are critically important to changing society and the efforts you, the player, make are the ones that really matter.
It's tacky, imo. The game shouldn't make the player feel good for baseline rebellion and morality, but rather challenge your ideas of what's acceptable and what needs to be challenged/stopped/changed.
And the game fails at that imo, it contradicts it's own messages left and right (look no further than Ann), it makes the player character the center of the universe to an obnoxious degree, and portrays real problems being committed by friggin' captain planet villains.
It's just a really clean, safe, valid game overall and that's more disappointing than any gay route could be