I tried to respond in the best way I could, feel free to ask more questions.
1. What happened to Morgana is a bit of a spoiler of the end, he went with Sojiro in secret, to get a vacation without the protagonist, it's kinda like a payback for Hawaii in his mind. For the girls, I thought about adding a place that you would be able take the party members for exploration and combat, but I feel like it's to late now, but I do plan on implementing that idea in the persona 3 game.
2. I agree, they will accept and be fine with the harem, I'm just waiting until there's no more girls left to add.
3.Not for this game, I don't think it fits, I could do an entirely futa game in the future, but right now I am very busy with my current projects.
4.Yes.
5.That's another thing that I'm implemething on the persona 3 game, but it's be more focused on the personas the player collects.
6.Those are glimpses of the future, and I like that idea of the final image, I already have something similar in mind myself.