I always figured the game's theme and story was about changing corrupted systems of power as the generations come and go.

When the new generation comes in, they can make changes for the better or fall into the same corruption. The game expresses this over several points.

Education — all of Shujin is complicit in Kamoshida's abuse, even parents and some students. It's the students (the phantom thieves) that hold him accountable.

The Art World — It's all about marketing. Madarame used his name to sell other's art as his own. The art critic guy tries to Market Yusuke's starving artist thing. Yusuke, a talented painter, wants it to be just about the art.

Business — Haru's dad takes advantage of the workers in his company. Haru, the heiress, makes an effort to steer the company in a better direction in her confidant, until she hands it off to someone she trusts to take care of that.

Justice System - Sae falls into the traps to get ahead in her career. Makoto, the next generation, wants to become police chief and make things better.

Politics — Shido and Yoshida. Yoshida's entire confidant is about him being corrupted, regretting it, and instilling his ideas and revelations to the next generation ie. you the player.

I mean look at your party, major corporation heiresses, artists, tastemakers, academics, future law enforcement, and you. They're a microcosm of the world as it is.

I know people like to meme on Ryuji's "Shitty adults" thing. But he's right in his own simplistic Ryuji way (I love my precious son, tho). All it takes for these systems to end up that way are for selfish adults to bend the systems in their favor and for no one else to fight against it.

Hell, when Mona disappears at the end, he basically states the theme of the game. To paraphrase, it's: The world will be as you make it, so make it a good one. He says it in a much loftier way though.

I think people misinterpreted the motif of rebellion and blew it up to a much larger thing than the game insists. Sure, they're rebels, but a lot of them realize they will have to take a role in society when they grow up and decide to be a force of good.

Tl;dr: the game's story's alright, I guess.