There are actually two different versions of the Balloon Fight stage. The layout is selected randomly, but the alternate form can be chosen by holding down the L button when selecting the stage.

Holding down the L button when selecting the Boxing Ring stage will change the design of the ring from Punch Out oriented to Super Smash Bros. oriented.

Having specific character pairs fight each other in a normal 1v1 Smash fight results in personalized victory screens:

• Fox beats Falco:"Better luck next time, Falco."
• Falco beats Fox: "You're off your game, Fox."
• Male Robin beats Lucina: "Lucina, I hope I didn't hurt you."
• Female Robin beats Lucina: "How can you protect Chrom if you can't protect yourself?"
• Lucina beats Marth: "This is the Hero-King?"
• Lucina beats Ike: "And they call you the Radiant Hero?"
• Palutena beats Pit:"Oh, so sorry about that, Pit."
• Palutena beats Dark Pit: "Poor little Pittoo."
• Dark Pit beats Pit: "Where's your goddess now?"

Leaked screenshots show that there was originally a trophy for Tharja from Fire Emblem Awakening, but it was removed from the final game. Some speculate this was because of her suggestive clothing that would have likely given the game a more mature rating from the ESRB. There has been no confirmation that this trophy was ever set to appear.

Holding down L before selecting the Dream Land stage in the 3DS version will cause the stage colors to change to black and white, instead of the usual black and green.

The Pokemon Trainer trophy makes reference to the first opening theme music from the English dub of the Pokémon anime.

"Pop quiz! What do Misty, Brock, Cynthia, Iris, and Ash all have in common? That's right"”they're all Pokémon Trainers! This Pokémon Master in the making is the same. Back in Super Smash Bros. Brawl, he fought to be the very best"”like no one ever was. To smash them was his real test"”to launch them was his cause!"

The song that plays on the results screen after a fight is the character select theme from the first Super Smash Bros.

Sometimes when Luigi uses the green missile and he hits a wall, he will stick to the wall.

Within the game's data are a number of unused images that would have been displayed in the game's tutorial section.

According to Masahiro Sakurai, the reason the Ice Climbers were cut from the roster is because of 3DS hardware limitations. He also states that he didn't want to add them exclusively to the Wii U roster to avoid there being considerable differences between the two versions.

According to series director Masahiro Sakurai, Dr. Mario, Dark Pit and Lucina were originally considered to be alternate costumes for Mario, Pit and Marth respectively, but were eventually changed to be their own separate characters with slight differences in their movesets from the three.

All of the characters in the game were chosen at the start of development. This means Geninja was chosen before Pokemon X & Y was released, and that its inclusion was not because of its popularity.

There was an open slot for a new Pokémon character, and the team began discussing who to put in it, eventually settling on Greninja. All the reference material they had for Greninja were simply drawings at that point. Sakurai went home the same day he received the Greninja reference material and stayed up until midnight to do the motion capture for the character.

The Smash Run mode was influenced by the City Trial mode in Kirby Air Ride.

When either of the Links are fighting, the Toon Link driving the Spirit Train is replaced with Alfonzo.

The Japanese trailer introducing Mega Man in Super Smash Bros. for 3DS and Wii U has "Clash Man" (the original Japanese name) instead of "Crash Man" (the English name) in the Japanese commercial, despite being changed to Crash Man in Japan.