1. That's a good point and something I considered. I originally planned to have Joker instead of Yu, but decided against it simply to help the game differentiate itself from Smash, which is something they'd really need to focus on.
You could say the same thing for Cloud and another Final Fantasy character, but Final Fantasy VII is just too huge and important to not only PS but gaming as a whole to ignore for someone like Tidus. Persona 5 didn't redefine what an RPG, or even just a game in general could be. It was just more popular than the last game in the series, just like P4 was to P3. I think it's fine to have Yu in the base game to differentiate from Smash, and have Joker as DLC.
2. I feel like there's no need to bring back Big Daddy and Isaac Clarke. They are in no way PlayStation icons and were only in the first game because Sony just tried to strike whatever deals they could to get more characters, and they were easy to get to promote a new game. Bioshock and Dead Space has simultaneous launches on PS#, 360, and PC. No clue why they were in in the first place.
3. I don't know how I didn't think of him, but I'd still pass as he represents the same exact game as Cloud. He'd be essential to the potential villain-themed sequel, or maybe he could even be DLC.