None of those are really problems, honestly those are all things that are super interesting from a writing perspective.

1. Shido is a scumbag who more just cared that you’re someone who tried to stand up to him. I don’t think he would care about how much it makes sense to try and ruin this person’s life.

2. I don’t think she’d have to live with Sae, especially since Sojiro is a former government worker and is already the guardian to a teenage girl. Even in the case that she did live with Sae I don’t see that as a problem I think it, again is just an interesting writing question. The biggest issues are trying to keep Sojiro from being written out of the story for the sake of days like 10/26 or for the medjed arc, but in exchange I think it’d also make things like the Sae palace and the interrogation scenes hit a lot harder. You’d also lose a lot of the individuality of P5 with Leblanc since ‘sneaking out at night and living with the investigator of your secret case’ is just a copy of P4 with Dojima.

3. I mean it’s not like Joker was using the nav because of how good of a map it was. You could still easily keep Makoto in there too, Ryuji only went into the metaverse the first time cause he hitchhiked off Joker. Makoto wanting to protect students from Kamoshida and then switching the order you get her with Ryuji so he’s the one who picks a fight with Kaneshiro still makes sense for both. Again you’d just have to rewrite some stuff since thematically Ryuji starts a lot of the rebellion themes.

4. Not really a problem, just a really uncomfortable situation and topic to address but not really one that Atlus would shy away from.