Well, since I got Joker, I'll start with him..
Route: Steal Your Heart
Joker would probably face off against sinful characters, possibly those that work with the sins of the boss characters in his home game..so...
Lust, Vanity, Gluttony/Greed, Wrath, Envy, Pride
His boss could be Marx since he's the closest to an evil god-like being and also resembles some Persona 5/Shin Megami Tensei enemies such as Jack Frost. Wario gets to pull double duty as a reference to both Kaneshiro (Gluttony) and Okumura (Greed).
Sora from Kingdom Hearts
Route: Sealing the Darkness
Sora's route would involve travelling to different worlds and getting rid of 'darkness', IE dark versions of characters akin to Link's. I don't know what order they'd be in, but I could see him travelling to different popular worlds like Mario, Sonic, Zelda, Pokémon, Metroid, and Street Fighter, fighting against characters using their black or dark colour alts, such as the darker coloured Black Alt for Sonic or Ryu & Ken in their Black Gi, perhaps fighting all three Dark Links (Normal, Young, Toon). His boss could follow Jigglypuff and Bayonetta and have him fight Ganondorf's White Alt in a giant form for its resemblance to Xehanort and Xemnas.
2B from NieR Automata
Route: Glory to Mankind
2B would face off against Robotic/Synthetic Characters to reference her battle with Machine Lifeforms, Adam & Eve, and other Androids. Mii Fighters using costumes remembling machines/robotics would be used, like the Power Lifter or LABO ones. The last main fight would be a mirror match against other 2Bs to reference (spoilers) and her boss would, of course, be Galleom.
(Horde),
(Horde)
:ult2B
Horde)