Well, hey, why not, guess I'll pitch in. Don't have anything better to do. For simplicity's sake, I'll only go up to 4 alts, max. Just alts for now. Maybe I'll do clones in a follow-up post. Right now, I'll do the original 12 (with some omitted that I couldn't think of anything for).
MARIO: MR VIDEO GAME HIMSELF
-Alt 1: Sunglasses and shirt from Super Mario Sunshine; one version with blue sunglasses, and the other with black sunglasses ala some Brawl mods
-Alt 2: Builder Mario (Super Mario Maker)
-Alt 3:
Rapper Mario (Super Mario Pinball commercial)
*Side note: In his current condition, Dr Mario should never become an alt of Mario. Two different moves alone and differing stats are plenty enough for a different slot on the roster.
DONKEY KONG: KING OF THE JUNGLE
-Alt: His outfit from his appearance as a secret boss in Punch-Out Wii
LINK: HERO OF HYRULE
*NOTE: Since everybody should know now he's rocking that Breath of the Wild look, this means that some of these may not work should Link be getting drastically altered.*
-Alt 1: His appearance from Brawl/SSB4
-Alt 2: Ocarina of Time Link (the one that appeared in 64 and Melee, also has voice clips from said games)
-Alt 3: Dark Link (He's an alternate form of a playable character just like Alph and the Koopalings; own announcer call, his name is listed as Dark Link, etc. Also, his sword, shield, and other weapons are aesthetically modified to resemble Dark Link's equivalents in the Zelda games. He is fully silent)
SAMUS: BOUNTY HUNTER EXTRAORDINAIRE
-Alt 1: Light Suit
-Alt 2: Fusion Suit
-Alt 3: Original Power Suit
-Alt 4: Dark Samus (Once again, full-fleged alt like Alph/The Koopalings. This would mean she couldn't be an assist trophy no more, but hey, playing as her is even better. Weapons altered to look more like Dark Samus' equivalents, and of course she has voice clips from the Metroid Prime series)
KIRBY: THE PINK PUFFBALL
-Alt 1: Shadow Kirby (once again, Alph/Koopalings styled alt; has his appearance from Kirby Triple Deluxe's Kirby Fighters mode. My friend was the one who came up with this, he's much more of a Kirby nerd than me)
FOX MCLOUD: LEADER OF STAR FOX
-Alt 1: Smash 64/Melee fox (with Melee voice clips)
-Alt 2: Star Fox Zero Design
PIKACHU: PIKA PIKA!
-Alt 1: A proper female Pikachu alt. Don't remember who suggested this, but thanks for the idea.
-Alt 2: Pikachu Libre
JIGGLYPUFF: THE SLEEPY SINGER
-Alt: Fairy Jigglypuff; because, y'know, she's a fairy type now.
LUIGI: THE ETERNAL UNDERSTUDY
-Alt 1: Mr. L
-Alt 2: Dr. Luigi
CAPTAIN FALCON: THE SUPERSONIC SLUGGER
-Alt: His appearance in the first F-Zero
NESS: THE PSI POWERHOUSE
-Alt: The pajamas he had at the beginning of Earthbound in the U.S