I remember thinking of ideas for that scenario as well, here’s what I had before:
Pair Units
Legend of Zelda: Zelda & Impa
Kid Icarus: Pit and Dark Pit
Shin Onigashima Kouhen: Donbe & Hikari
Kaeru no Tame ni Kane wa Naru: Prince of Sablé
Fire Emblem: Eliwood and Hector, Alm & Celica,
Sin & Punishment: Saki and Airan
Golden Sun: Isaac and Felix
Zangeki no Reginleiv: Frey and Freya
Xenoblade Chronicles: Rex & Pyra, Nia & Dromarch,
ARMS: Spring Man and Ribbon Girl
Solo Units
Legend of Zelda: Link (uses Navi to communicate)
Metroid: Samus Aran
Punch Out: Little Mac (uses Doc Louis to communicate)
Kid Icarus: Magnus, Phosphora
The Mysterious Murasame Castle: Takamaru
Advance Wars: Andy
F-Zero: Captain Falcon
Fire Emblem: Marth, Ike, Tiki, Lyn
Custom Robo: Ray MK III
Captain Rainbow: Captain Rainbow
Xenoblade Chronicles: Elma
Can't help but notice a lot of Fire emblem on here lol
Yeah I like the idea of having Andy and Takamaru as solo units. That's works pretty well.
As for the other companies X zone tends to have I picture some new additions like this
Pair units:
Joker and one of the female phantom thieves (it would be Kasumi but I'm more into Makoto)
Kite returning from previous titles but his partner is Megaman.EXE because the both of them are cyber space heroes
Replace Kiryu and Majima with Ichiban and one of his friends from Yakuza 7. I can imagine Ichiban getting all psyched up about going on a multiverse adventure just like in one of his japanese anime.
Solo units:
Both x zone games have 4 Street fighter reps while Ryu, Ken and Chun li are shared between the games the fourth one was swapped so continue that and bring in a character who's relevant to the SF5/3 era, like ibuki.
Vyse from Skies of Arcadia, once he meets Reiji they reference how he worked with the Valkiria chronicles 3 party since Reiji knows them.
Sakura from the new Sakura wars, remove Erica and Gemini and keep Ogami and OG Sakura.
Megaman zero, because he's cool.