One idea I've had when it comes to bringing back Break the targets with a large roster is instead of having each character get their own stage, maybe each franchise gets their own or each kind of class of character.
Like, they could have a Mario themed Break the targets that all Mario characters go to, and the stage is big and has multiple paths that work better depending on what character you use.
Same thing for Zelda, Pokemon, Fire Emblem, the retro NES characters.
I guess franchises with only one character (ie Splatoon and ARMS) that aren't retro NES could all share one and they could just pull a PSASBR and have a Break the Target stage that meshes their worlds together.