I'll try to set up a reasonable roster, with almost no goof-ups.
Super Mario
Mario
Luigi
Peach
Bowser
Bowser Jr.
Donkey Kong
Donkey Kong
Diddy Kong
Dixie Kong
King K. Rool
The Legend of Zelda
Link
Zelda / Sheik
Ganondorf
Toon Link
Metroid
Samus / Zero Suit Samus
Ridley
Yoshi
Yoshi
Kirby
Kirby
Meta Knight
King Dedede
Star Fox
Fox McCloud
Falco Lombardi
Wolf O'Donnell
Leon Powalski
Pokemon
Pikachu
Jigglypuff
Pokemon Trainer (Oshawott, Servine, Emboar)
Zoroark
F-Zero
Captain Falcon
Samurai Goroh
Black Shadow
EarthBound / Mother
Ness
Lucas
Fire Emblem
Marth
Ike
Kid Icarus
Pit
Wario
Wario
Pikmin
Olimar
Golden Sun
Isaac
Sin and Punishment
Saki
The Legendary Starfy
Starfy
Nintendo Classics
Ice Climbers
Mr. Game & Watch
R.O.B.
Bubbles
Eggplant Man
Takamaru
If 3rd parties were to be involved, I'd go with Sega and Square Enix. Sorry Konami, sorry Solid Snake. I also limited the number of 3rd party fighters by having only two characters per franchise.
Sonic the Hedgehog
Sonic
Tails
Final Fantasy
White Mage
Black Mage
Without the 3rd parties, roster adds up to 46 characters without the transformations. Add the 3rd parties, 50. Include the transformations, 55.