Man, this question unlocks a whole cabinet of tropes in the fandom. The classic twist is, of course, Jaune Arc the secret Targaryen, or whatever the Remnant equivalent would be. Like, he's a lost heir to some fallen kingdom like Mantle or even the old Arc lineage being way more noble and powerful than anyone thought. This lets authors give him a hidden reserve of power or influence he's been hiding out of fear or duty. Another huge one is the 'Jaune raised by X' scenario, where the twist is he wasn't raised by his family at all—he was trained by Salem, or Qrow, or even a completely different faction like the White Fang or Atlas Special Operatives. The plot twist is him revealing skills and knowledge that completely shatter Team JNPR's perception of their 'lovable dork' leader, often during a high-stakes battle.
There's also the 'Jaune is a reincarnation' angle, which overlaps with crossovers. The twist isn't just that he has memories of another life, but that the other life is someone like, I dunno, a legendary Huntsman from the Great War, or a villain from another series altogether. It's less about secret lineage and more about secret identity from a past existence that starts bleeding into his current one. And then you have the more subtle psychological twists, where Jaune isn't hiding a grand destiny but a dark past—like he was actually a runaway criminal, or he's the sole survivor of a Grimm attack that wasn't an accident but a targeted assassination attempt his family covered up. The drama comes from that secret guilt shaping his 'heroic' facade.
My personal favorite is the 'double life' setup where he's secretly a prolific information broker or vigilante with a separate alias that the whole underworld fears, while still being the awkward guy at Beacon. The plot twist is when his two worlds collide, and Ruby or Pyrrha puts the pieces together from some offhand comment or fighting style. It's less about epic power scaling and more about the personal betrayal and the 'who even are you?' moment.