Big main series icons that are still missing:
Toad or Captain Toad(but not both): Most well recognised character left from Nintendo, has starred in at least six games: Wario's Woods NES, Wario's Woods SNES, Captain Toad Treasure Tracker and it's two ports to Switch and 3DS and the Japan exclusive Satella-Q, used extensively by Nintendo as a mascot character. Is the only character used heavily in adverts for Nintendo products that has yet to make the leap to playable in Smash. Once made it into
Japan's top 100 video games of all time at number 8. The second most popular Mario Kart character after Yoshi. His resume is pretty impressive.
Toadette: Rising star. Between starring roles in Mario Maker 2, New Super Mario Bros. U Deluxe and Captain Toad Treasure Tracker, her playable roles are more impressive than any other female Mario character outside Peach.
Waluigi: Say what you will about him, but Waluigi IS popular and people want him in Smash.
Paper Mario: Heads his own successful franchise. A more impressive and unique Mario than Doctor.
Dixie Kong: The tritagonist of the Donkey Kong series. Had her own starring game. Recent success with Tropical Freeze
Cranky Kong: Between being the original DK, a new starring role in Tropical Freeze and even Cranky Rabbid, Cranky's got a decent resume.
Skull Kid: The most iconic Zelda antagonist after Ganon/dorf. The Majora's mask has become a staple in pop culture regarding Zelda.
Tingle: Love him or hate him, Tingle has his own games and is the most reoccurring character in the franchise outside the triforce trio, Impa and maybe Epona.
Impa: This one's more personal, but I feel Impa's roles within Skyward Sword and Hyrule Warriors made her a pretty good choice for Zelda.
(Honestly though you could include Midna or Tetra instead since they're also huge characters in the Zelda series that resonated with fans)
Bandana Waddle Dee: The fourth in the Kirby cast, and Waddle Dee are INSANELY popular in Japan to the point they seem to have more merchandise than either Dedede or Metaknight.
Dark Matter: The closest thing to a true villain in Kirby I can think of.
Krystal: Fan favourite
Slippy: Starred in his own game; Star Fox Guard which was, according to some, superior to Star Fox Zero the game it came packaged with.
Lyndis: Most popular Fire Emblem character overall apart from Ike, easily the most popular female Fire Emblem character.
Meowth: Main antagonist of the super popular anime. Recently appeared in the Let's Go games
Eevee: Probably the most popular Pokemon left. Constantly used in merchandise, starred in TWO games where it was a starter; Let's Go Eevee and Pokemon XD.
Blaziken: Incredibly popular Gen 3 Pokemon. Starred in Pokken.
Tom Nook: The original Animal Crossing mascot prior to Isabelle taking over. Tom Nook was the star of the show in the original games.
Kinda neat main series extras and nicher series:
Porky: Whilst Mother is still pretty niche, Porky connects Earthbound and Mother 3 together nicely
Medusa: Kid Icarus' main antagonist. Yeah, ***** to Hades.
Ashley: Very popular in Japan.
Midna: Very popular Zelda character(could easily be bumped up to missing icon or replace one of the Zelda cast up there)
Tetra: Very popular Zelda character(see Midna above)
Isaac: Ridiculously popular in the Smash circle, one of the few Nintendo IPs not represented as a character or stage
Saki: Less so than Isaac, but Sin and Punishment was at least notable enough to get a sequel
Chorus Kids: Rhythm Heaven's pretty big. A lot of people wanted these guys.
Chibi-Robo: Taken before his time, Chibi's adorable and his games aside from Zip Lash were beloved.
Dillon: Rolling Western was very niche but it has a decent fanbase.
Louie: Pikmin isn't super niche but Louie could offer something fresh to it with a bug based moveset
Lip: Mostly forgotten retro, replaced by Yoshi in the west, Lip's still got a vocal fanbase.
Takamaru: The defacto popular choice for a retro character
Mach Rider: The other, other popular retro choice.
Balloon Fighter: One of the most famous retro Nintendo games of all time.