Shido had Naoto's parents killed
Their death in a car accident fits the Antisocial Force's preferred MO, and as famous detectives, they may have been getting close to uncovering the conspiracy. Wakaba has a palace
Her repetitions in her journals of how she needs to be perfect are definitely starting to sound like a distorted desire. Yes, she's already accepted her shadow and gained a persona, but P5 Royal established that persona users can still have palaces, especially when they're well-versed in cognitive psience. Also, if she's still alive as the fic has been hinting, Futaba should be in a better place emotionally and not need the Thieves to steal her heart — though she might need them to steal her mother's heart. The remaining Arcana
The most likely arrangement is Makoto as the Empress (being a student council president like previous Empress Mitsuru), Futaba as the Devil (befitting her Alibaba profile picture and mischievous nature), and Teddie as the Chariot (being one of the only characters who can freely get himself in and out of the Metaverse). There's also the possibility that Makoto will be the chariot because of Johanna, Futaba the Empress because of her control over the internet, and Teddie the Devil if he hasn't gotten over his perverted ways yet.- As of chapter 370, Makoto has been confirmed as the Empress.
Nanako is Ren's Faith Arcana
Yoshizawa isn't present in the AU, but Ren has all his other confidants, making it likely that Nanako fills the role of the expansion love interest for him.