Did some Classic routes for my 3 most wanted of the Square 7. I'm only working with what we know and won't include stages and characters we don't currently have.
Geno: Repairing the Star Road
Each stage represents a location a Star Piece was found.
Stage 1: Joker on Princess Peach's Castle
We don't know for sure yet but I think Joker will have his knife.
Stage 2: Dark Pit on Dream Land
Closest thing we have to a forest that isn't a jungle, ironically Reset Bomb Forest doesn't fit aesthetically in either of its two forms.
Stage 3: Snake on Great Cave Offensive
Thought about the Links but went with Snake since he's more about explosives than they are.
Stage 4: Yoshi Team on Mario Galaxy
The Gecko enemies of Star Hill. Fairly easy, like how the location has no boss in the original game.
Stage 5: Corrin on Tortimer Island
Fight a spear user on a seaside town.
Stage 6: Simon x5 on Halberd. Assisted by Mario and Peach.
All 5 are color coded the closest they can get to Red, Yellow, Green, Pink, and Black.
Bonus Stage
Boss Stage: Giant King Dedede on the Omega form of Wrecking Crew, then Master Hand on Final Destination
I looked over our current cast for anyone who creates weapons, none of them do so I went with a hammer user. The two stages represent both parts of the Smithy fight.
Erdrick: The Legendary Hero
Erdrick fights characters whose actions are spoken of in legends, or are described as "legendary".
Stage 1: Young Link and Ganondorf on Hyrule Castle. Assisted by Toon Link.
Link from The Legend of Zelda: The Wind Waker grew up hearing about the Hero of Time, and also has to fight the Ganondorf from the same time period, who was the reason the goddesses flooded Hyrule in the present.
Stage 2: Marth and Ike on Castle Siege. Assisted by Lucina.
Marth is known throughout the Fire Emblem series as the legendary Hero-King. Ike is similarly famous as the Radiant Hero of legend. Marth is a legendary figure in Fire Emblem: Awakening's present and doomed future, who Lucina names her disguise after.
Stage 3: Snake on Shadow Moses Island
The Legendary Mercenary is also a legacy character, with the title of Snake being handed down to different people.
Stage 4: Mega Man on Wily Castle
The title of "Mega Man" is similarly passed down and / or given to new robots. His final Smash is also called "Mega Legends" and summons 4 of his successors.
Stage 5: Mewtwo on Pokémon Stadium
The only playable Legendary Pokémon.
Stage 6: Erdrick on Battlefield
This Erdrick has the opposite gender of the one you chose. I'm sure a DQ stage would come with Erdrick but I dunno for sure so I defaulted to Battlefield.
Bonus Stage
Boss Stage: Dracula
I thought about making the fight reference Baramos and Zoma with other characters, but I decided I wanted a boss as a legendary figure instead, and Dracula's the one with the most clout behind him. Dracula pulls double duty as the Dragon Quest staple of "final boss with multiple forms" like the Dragonlord, and hating light like Zoma does.
Crono: To Far Away Times
Each stage represents a different time period, as well as the party members associated with them.
Stage 1: Purple Inkling and Yellow Lucina on Smashville. Assisted by Crono.
The Millenium Fair and 1000 AD. K. K. Slider plays here no matter what day or time it is. Purple Inkling is Lucca who attacks with guns, and Lucina is in her Lissa color, being a nice princess who knows how to fight.
Stage 2: Green Greninja on Hyrule Castle
Guardia Castle and 600 AD. Greninja already has water swords (well, they're kunai now) so he fits Frog to a tee.
Stage 3: Yellow R.O.B. on Midgar
The ruined future of 2300 AD.
Stage 4: Crono on Final Destination
The End of Time. No party members are recruited here so Crono is fought here in a ditto match.
Stage 5: Purple Peach on Kongo Jungle
This stage has 65,000,000 BC's general jungle aesthetic. Peach was chosen since she's the most physical of the female fighters that doesn't use a weapon.
Stage 6: Dark Pit on Fountain of Dreams
The Ocean Palace of 12,000 BC. Fountain of Dreams was chosen since it has a magical air about it compared to other water themed stages.
Bonus Stage
Boss Stage: Master Hand and Crazy Hand on the omega form of New Donk City
Represents the final boss at 1999 AD.