The Official List of Suggested Characters:

All taken from Toukouken!. Remember, this isn't a popularity poll; just a collection of selected comments submitted to the site and printed for various reasons (some are obviously jokes). Just because a character does not appear on this list doesn't mean they won't be in the game (as well as the opposite). The number beside each character indicates the number of comments posted suggesting them:

Mario Bros.
Banker (Mario Paint)<1>
Blue Virus (Dr. Mario)<1>
Chain Chomp (AKA Bow-Wow in LoZ: Link's Awakening)<1>
Geno (Super Mario RPG)<4>
Hammer Bros.<1>
Koopa Troopa<1>
Mallow (Super Mario RPG)<1>
Para Troopa<1>
Petey Piranah (Super Mario Sunshine)<1>
Toad<1>
Vivian (Paper Mario & The Thousand Year Door)<1>

Donkey Kong
Diddy Kong<4> (Diddy & Dixie team also counted)
Dixie Kong (with Diddy Kong)<1>
King K. Rool<2>
Rambi<1>
Zinger<1>

Legend of Zelda
Cuckoos<1>
Link in The Windwaker<3>
Link's Uncle from A Link to the Past<1>
Navi<1>
Tetra<1>

Metroid
Noxus (Metroid Prime: Hunters)<1>
Ridley<4>
Sylux(Metroid Prime: Hunters)<1>
Weavel(Metroid Prime: Hunters)<1>

Kirby
King Dedede<5>
Lololo & Lalala<1>
Marx (Kirby Super Star)<1>

Star Fox
Krystal<3>
Peppy<1>
Slippy<1>
Wolf O'Donnell<1>

Pokemon
Gardevoir<1>
Steven Stone (Ruby & Sapphire)<1>

F-Zero
Black Shadow<1>

Earthbound/Mother
Claus (Mother 3)<2>
Jeff (Earthbound)<2>
Kumatora (Mother 3)<1>
Lucas (Mother 3)<2>
Ninten (Mother/Earthbound Zero)<1>
Paula (Earthbound)<1>
Poo (Earthbound)<1>

Fire Emblem
Black Knight (Path of Radiance)<1>
Ike (Path of Radiance)<4>
Jeigan (Ankoku Ryū to Hikari no Tsurugi)<1>
Maji (Ankoku Ryū to Hikari no Tsurugi)<1>
Mia (Path of Radiance)<1>
Navarre (Ankoku Ryū to Hikari no Tsurugi)<1>
Oguma (Ankoku Ryū to Hikari no Tsurugi)<2>
Saji (Ankoku Ryū to Hikari no Tsurugi)<1>
Sheeda (Ankoku Ryū to Hikari no Tsurugi)<1>
Sigurd (Seisen no Keifu)<1>
Soren (Path of Radiance)<1>

Other Nintendo Games
Captain Olimar & Pikmin (Pikmin)<3> (Entries for both counted)
Chibi Robo<1>
Demiru (Tomato Adventure)<2>
Donbe (Shin Oni Go Shima)<1>
Dragon Chan (Super Punch-Out!!)<1>
Dr. Wright (Sim City SNES)<1>
Eggplant Wizard (Kid Icarus)<2>
Felix (Golden Sun)<1>
Furil (Ninteno Puzzle Collection version of Panel de Pon)<1>
Harry (Teleroboxer)<1>
Infantry (Famicom Wars)<1>
Isaac (Golden Sun)<2>
Jill (Drill Dozer)<1>
Lip (Panel De Pon/Tetris Attack)<2>
Little Mac (Mike Tyson's Punch-Out!!)<1>
Main Character of Animal Crossing<2>
Main Character of Maical Vacation<1>
Medusa (Kid Icarus)<1>
Muddy (Mole Mania)<1>
Ouendan! (Osu! Tatakae! Ouendan!)<2>
Palutena (Kid Icarus)<1>
Professor Kawasima (Brain Age)<2>
Ray 01 (Custom Robo)<1>
Sukapon (Joy Mecha Fight)<2>
Takamaru (Nazo no Murasame-jo)<2>
Tomato Robot (Tomato Adventure)<1>
Tom Nook (Animal Crossing)<1>
Urban Champion<1>

3rd Party
Colonel volgin (Metal Gear Solid 3, Konami)<1>
G-Red (Gotcha Force, Capcom)<1>
James Bond (007 Games, the estate of Ian Fleming)
Kalas (Baten Kaitos, Namco)<1>
Katia (Last Kingdoms, From Software)<1>
Lupus (Jet Force Gemini, Rare)<1>
Magnus (Ogre Battle 64, Quest(now owned by Square Enix)/Atlus)<1>
Mega Man (Mega Man, Capcom)<2>
Pawapuro-Kun (Power Pro Baseball, Konami)<1>
Simon Belmont (Castlevania, Konami)<1>
Sora (Kingdom Hearts, Square Enix)<1>
Thomas(Kung-Fu, Irem, based on Jackie Chan movie Spartan X)<1>