I loved Fuuka's reserved nature. She was adorable and her quirk of being horrible at cooking was cute, as well. Sure, her voice-acting in Persona 3 was a bit shaky. But her personality and voice were reworked a bit in Persona Q and it helped her climb the ladder of favorites for me. She's definitely the best out of all three, personality wise. I love her design, her Persona's design, her social link, her dynamic with the main cast and just her overall appeal.
Futaba was endearing and I related a lot to her behavior. She's a genius and a huge driving force in the team. Her support in battle helped me when I was in a pinch and her social link both made me laugh and tugged at my heartstrings from how I understood her plight. She's my second favorite, but only by a small amount. If Fuuka was any less what she is, Futaba would easily be first place.
As for Rise, I was unfortunately never a big fan of her. There's nothing wrong with her, per say. Her optimism and talent is quite entertaining. However, her backstory, motivation, etc, didn't hit me quite as hard as it did with Fuuka and Futaba. Third place, but I feel guilty saying so.