The game originally had a 4th set of custom moves for all characters. By hacking the game it is possible to activate them, although most of the moves are unfinished, and do not deliver damage.

The dollar bills that are collected in the Wii U's Coin Battle mode have an image of Nintendo's Japanese Headquarters printed on them, as well as a photo and signature of series creator/director; Masahiro Sakurai.

The only virtual console game that doesn't appear within the masterpieces menu in the International release of the game is "Fire Emblem: Shadow Dragon and the Blade of Light", as this title was never translated or released anywhere but in Japan.

In Super Smash Bros for Wii U the trophy titled "Hocotate Bomb" states that it appears in Pikmin and Pikmin 2 even though it appears in Pikmin 2 and Pikmin 3.

This is the first time both Master Hand and Crazy Hand have in-game announcer calls that are used.

Kongo Jungle is the only past stage from the original game to return, with the exception of DLC.

Some of the Boxing Ring Stage titles contain references and easter eggs.

Luigi's, "The Eternal Understudy", is a reference to his unlock screen in the original Super Smash Bros..

Fox's title in the European version "Never Gives Up! Trusts His Instincts!" is a reference to a line in Starfox 64 said by Peppy in the Asteroid Belt level (and later on said by Fox's father).

Kirby's European title "Gritty in Pink" is a reference to the movie "Pretty in Pink".

Sonic's European title "Speed is his Game" is a reference to one his popular quotes "Sonic's the Name, Speed's My Game!".

Pikachu and Jigglypuff's European titles are actually just their Pokedex names.

Mewtwo's title "The Legend Reawakens" is a reference to the title of the Pokemon anime movie "Genesect & The Legend Reawakens".

Lucas' European title "The Tazmilian Devil" is reference to the Tasmanian Devil.

Roy's title "The Young Lion" references the title given to him at the end of Fire Emblem: The Binding Blade.

The Hyrule Temple stage has Hylian text written along many platforms that when translated to English reads "Smash Brothers". This was illegible in previous appearances of the stage.

Many of the Boxing ring titles were changed when the game was brought to the PAL Region:
• Mario: "Mr. Video Game Himself" became "Smashes Bricks with his Fist."
• Luigi: "The Eternal Understudy" became "Lean, Green Fighting Machine."
• Peach: "Princess of Toadstools" became "Princess of the Mushroom Kingdom."
• Bowser Jr.: "The Prince of Koopas" became "Like Father, Like Son."
• Larry Koopa: "The Youngest" became "Leader of the Seven Minions."
• Roy Koopa: "The Cool One" became "Fear the Shades."
• Wendy Koopa: "The Bold Beauty" became "Bold, Bossy, and Big-Headed."
• Morton Koopa: "The Enforcer" became "He'll Make You See Stars."
• Lemmy Koopa: "Wacky War Machine" became "Let's Get Wacky."
• Yoshi: "Omnivore of the Year" became "He's Not Yolking Around."
• Diddy Kong: "The Acrobat" became "Trigger Happy with His Peanut Popgun."
• Little Mac: "Bruiser from the Bronx" became "The Only Numbers He Knows Are 'One-Two'."
• Sheik: "The Illusive Sheikah" became "A Sheikah Shrouded In Mystery."
• Ganondorf: "The King of Darkness" became "The King of Evil."
• Toon Link: "Wind-Waking Warrior" became "Wave-Riding, Wind-Waking Warrior".
• Zero Suit Samus: "The Warrior Within" became "Low Armour, High Agility".
• Pit: "Captain of Lady Palutena's Guard" became "Lady Palutena's Captain of the Guard".
• Marth: "The Hero-King" became "The Legendary Hero-King."
• Ike: "The Radiant Hero of Legend" became "The Radiant Hero".
• Robin: "The Tactician Magician" became "The Tome-Toting Strategist".
• Kirby: "The Pink Puffball" became "Gritty in Pink".
• Duck Hunt (Duo): "Bark, Quack, Boom!" became "The Most Unlikely of Partnerships".
• King Dedede: "The King of Dream Land" became "Says He's King, and That's That".
• Fox: "Leader of Star Fox: became "Never Gives Up! Trusts His Instincts!".
• Pikachu: "Pika Pika!" became "The Electric Mouse Pokemon".
• Lucario: "Master of Aura" became "Exudes Power".
• Jigglypuff: "The Sleepy Singer" became "The Delightful Balloon Pokemon".
• Greninja: "Master of Stealth" became "The Unpredictable Ninja Pokemon".
• R.O.B.: "The Last of His Kind" became "Robotic Obliterating Buddy".
• Captain Falcon: "The Supersonic Slugger" became "The Supersonic F-Zero Pilot".
• Wii Fit Trainer (F): "The Yoga Warrior" became "She'll Make You Feel The Burn!".
• Shulk: "The Visionary" became "Has Visions of Victory".
• Dr. Mario: "The Prescriber" became "Fists Full of Medicine".
• Lucina: "Warrior from a Doomed Future" became "Defiant of Destiny".
• Pac-Man: "The Yellow Bane of Ghosts" became "Ghost-Gobbler".
• Mega Man: "Blue Metal Hero" became "The Blue Bomber".
• Sonic: "The Blue Blur" became "Speed is His Game".
• Lucas: "The Boy From Nowhere" became "The Tazmilian Devil"
• Wii Fit Trainer (M): "The BMI Bandit" became "He'll Blast Your Core!".
• Alph: "Astronaut in Training" became "Novice Explorer, Engineering Pro".

This is the only game in which Kirby doesn't have a new dash attack, but instead reuses the one from Super Smash Bros. Brawl.

According to Masahiro Sakurai, Bowser Jr. was very close to not being included in the game's roster.

In international releases of the game, the Porky Minch trophy's game chronology only mentions his appearance in EarthBound and not Mother 3, even though the trophy description mentions both games and the trophy's design is taken from Mother 3.

Metal characters reflect daytime Town and City, even at night.

Bowser is the only veteran in the game to not have his victory theme ripped straight from Super Smash Bros. Brawl.

Chrom was originally intended to be a playable character in the game, but was replaced with Robin as Sakurai thought he'd play too similar to Marth and Ike, and that Robin would be a more unique character. Chrom still however appeared as a part of Robin's Final Smash, and did become playable in the next game in the franchise, Ultimate

During the song "Master Core" (which plays when fighting the identically-named boss in Classic Mode), the instruments will silence after 1 minute and 53 seconds and a series of beeps will play for six seconds before the instruments start playing again. These beeps are Morse Code for "MASTER CORE".

If Shulk is on the Gaur Plains stage when Metal Face appears, Metal Face will occasionally say unique taunts.

The taunts are:
• "If it isn't the puny boy himself.You miss me?"
• "Hey, Monado boy, I don't think you can hurt me with that thing"
• "OH! It looks like Monado boy's been practicing"
• "If the brat's here, I bet Dunban can't be far behind."

The amiibo figures sold alongside the game are well known for having a number of defect units. These include, but are likely not limited to:
• Samus having 2 cannons instead of 1.
• Marth having 2 swords instead of 1.
• Peach having no legs.
• Luigi missing his left hand.

When Pit gets KO'd he'll sometimes say, "I'm Finished". This is a reference to the original Kid Icarus Game Over screen.

In the Boxing Ring stage of the Wii U version of the game, character aliases appear on the screen in the background which reference other games or early concepts, such as Mario's being "Mr. Video Game Himself" referencing his early name "Mr. Video", and R.O.B.'s being Spoiler:"The Last of His Kind", referencing the events of Subspace Emissary from Super Smash Bros. Brawl in which Spoiler:the other R.O.B.s were destroyed.