Long ago, AEM said he would update this.
-And today is a day where things are being updated!!
Super Mario
- Paper Mario now uses his trophy model from the 3DS version.
The Legend of Zelda
- Young Link, Ganon, and Worlds Link icons have been updated.
- Overall visual improvement for several icons.
Metroid
- Ridley is an enemy character.
- Meta Ridley and Anthony don't appear in the games.
- Adam is a trophy.
Yoshi's Island
- Kamek is an enemy character.
- Baby Mario and Baby Luigi are trophies.
Kirby's Dreamland
- Magolor is a trophy.
- (Bandana) Waddle Dee and Dark Matter do not appear in the games.
Pokémon
- Female Pokémon Trainer was removed from the chart to make it appear cleaner.
- Jigglypuff was confirmed to be playable.
- Mewtwo was confirmed to eventually be playable as DLC.
- Zoroark was confirmed to be an assist character.
- Pichu, Pokémon Trainer, Squirtle, Ivysaur, Blaziken, and Mega Blaziken are trophies.
- Mega Mewtwo X and Mega Mewtwo Y are trophies, but their role may change once Mewtwo is playable.
- Sceptile, Plusle & Minun, Mega Charizard Y, and Mega Sceptile do not appear in the games.
- Several artwork updates.
MOTHER
- Ness is playable.
- Lucas and Porky are trophies.
- Ninten appears in Magicant.
- Claus is not in the games.
Fire Emblem
- Anna is a trophy.
- Roy does not appear in the games.
WarioWare
- Wario is a playable character.
- Wario-Man is Wario's final smash, and is playable through those means.
- 9-Volt and Mona are trophies.
- Jimmy T. appears in the Gamer stage.
- Captain Syrup does not appear in the games.
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I also updated the OP slightly to list out what role each character on the list has in the games. So good stuff. Will probably update again when I finish the rest of lists, just need to find all of those 3DS trophies again s: