No more FE, and to that effect just balancing the franchise representation in general. I'm on the autistic spectrum, and a way that affects me is that it physically bothers me to see series like Fire Emblem and Kid Icarus have more characters than Animal Crossing and Pikmin, so I'd want to balance that more fairly. I don't really know how I'd go about doing this without digging into Wikipedia or exact sales numbers or somesuch nonsense, but I just think a "Nintendo All-Star Fighting Game" should focus on the big stuff: Mario, Zelda, DK, Kirby, Pokemon, Metroid, Star Fox. Make sure these big iconic brands are well-represented before you dip into the FE well again and again and again. Smash 4 was the first game in the series that truly threw this out the window, which is fine and pleased many people, but just isn't what I would do if I ruled the world.
I know this isn't entirely logical and many franchises just don't have a lot to work with character-wise (Pikmin has one kind of playable character all of whom play the exact same, and all the enemies are drones) but I still think improvements could be made in this category. DK and Zelda should have more than Fire Emblem.
All that being said, if I were in charge I'd cut down the third parties as well, of course, limiting them to just ones that are very Nintendo-associated. Naturally I'd keep Sonic, Mega Man, and Simon Belmont (maybe Bayonetta as well, but she's basically Nintendo). The others...just kind of bother me, even to this day. I'm happy for the people who wanted Cloud, but boy does his presence make me uncomfortable.
Rayman is a big personal pick of mine, but that is an entirely selfish choice because of a lifetime fandom; I know he's got jack to do with Nintendo.