The general themes of the game and series are -far- deeper than most - the real dark areas of a theme are explored through a Social Link or a month or so of game time. Early on, the dream of being a princess in a castle waiting for her Prince Charming is thoroughly explored for realism, not for fantasy ideals, and it's darkly funny.
Searching for the truth is a rough subject, anyways, and the rating allows for the full impact to be depicted in each situation. It just might be that the graphics being "cartoony" are what prevent the game from being slapped with an AO and having to dumb itself down to fit an M... after the PS1 version of the first Persona, nobody wants a half-butchered SMT game. --- ...as opposed to an average game.
As others have said, it's the giant dick in the chariot flailing it's hands and tentacles. And corpses hanging on telephone poles.
Also the sexual innuendo of some dungeons, maybe.
But even without all that, a giant flailing penis on wheels was probably more than enough. And now that I'm thinking about it, I just realized Mara has a mouth, and that creeps me the hell out. Big green wang? Cool. Riding a chariot? Cool. With hands and tentacles? Whatever. And it has a weirdly human mouth? NOPE. --- Look! The East is burning red!