The Wii U version contains unused sounds of Kirby saying "Heavenly Light" and "Explosive Flame", both of which are Palutena's custom Neutral Specials, suggesting that he was originally intended to copy the custom standard specials of other characters.

In the Japanese version, Wonder Pink's trophy had a different pose, and her legs and underwear were shaded to make it appropriate for the CERO rating.

The emulated NES demos featured in the "Masterpiece" collection seem to run NES games at a higher quality than the actual Virtual Console versions they are promoting. This is most evident in how smooth and clear these demos look against the comparatively blurry VC ports.

This is likely due to Nintendo's improved emulation abilities rather than them purposefully trying to mislead fans, as the NES Virtual console was released very early in the Wii U's lifespan and likely used a system similar to that of the Wii.

Underneath Link's hat, you can see fully modeled hair that cannot be seen under normal circumstances.

According to Masahiro Sakurai, in the November 2014 issue of GameInformer, the reason why Super Smash Bros. was released on two different consoles was because he was a “freelance game designer,” and that having a unique version of the game makes it fun.

"The first reason is that I think both portables and home consoles have their own traits that make them fun. I've gone into that in previous interviews, so I'll omit the details here.

One big reason for this approach is because I'm a freelance game designer ... I'm always going to be the center of any Smash Bros. project, but since I don't have my own personal studio, the staff changes in and out with each project. Changing development studios like this also means that you can't build out from the know-how and in-house assets you've accumulated over time.

As a development environment, it's different from a publisher that can work on fighting games, shooters, and open-world titles all at once. For us, even if things look the same, it's all completely different, completely built from scratch. If we started with a console project then moved on to the portable platform, once one team finished up their work, we'd have to wait and hand everything over to another team."

According to Masahiro Sakurai, in the November 2014 issue of GameInformer, the reason why both versions were released at different times was done to "keep the debugging schedules separate from each other:"

"The biggest reason was so we could keep the debug schedule separate from each other. Debugging a game this size is a major project involving hundreds of people, and since the two platforms offer pretty different content, we wanted to avoid conflicts during the debug stages. If we were hell-bent on a simultaneous day-and-date release, we would have wrapped up one title, put it on the back burner, and launched both games in 2015. But I doubt most people prefer that."

Xander Mobus, the game's announcer, has stated that he had difficulty pronouncing Jigglypuff's Japanese name, Purin.

Roll's trophy contains modeled and textured undergarments beneath her dress; however, this is obscured in typical gameplay by a black void. This notably differs from Peach's trophy, which features similar censorship but has the black void baked into the model (with no additional graphics hidden underneath).

Donkey Kong's sprite on 75M in Super Smash Bros. Brawl and Super Smash Bros. for Wii U has a tan skin tone, which is different from DK's paler sprite in either the NES or arcade versions of Donkey Kong. This appears to be the result of Nintendo using an image of the game's arcade version originating from a Japanese retro gaming fan site called Muu-World as reference material, as that image seems to have a color error that makes DK appear tan. The English-language fan wiki Super Mario Wiki has been hosting a different Donkey Kong screenshot with the same error on its page for the game since 2005, and the source of the error as well as several of the images featuring it (including the Mario Wiki screenshot) is currently unknown. It also gives DK a coincidental resemblance to the appearance on the box art for NES Donkey Kong and in-game in Atarisoft's Commodore 64 Donkey Kong. This was fixed for Super Smash Bros. Ultimate.

The first Aparoid boss of Star Fox: Assault is a giant butterfly looking creature that appears at the end of the Fortuna mission. This particular Aparoid would reappear as a trophy in Super Smash Bros. for Wii U and also a spirit in Super Smash Bros. Ultimate, in both cases being dubbed simply as just "Aparoid".

The official Japanese Star Fox: Assault guidebook reveals this type of Aparoid to have a proper name: ゼグダリア (Zegudaria), or Zegdahlia as it's called by the provided English text.

Some of the Aparoid infected Cornerian ships that appear in Star Fox: Assault's campaign look very similar in design to its iteration of the Arwing. This is because, canonically, they actually are said to be mass produced Arwing models, according to both the official Japanese guidebook (where are they are given the fitting name of "P.A.W.N") and also the "Arwing (Assault)" trophy description in Super Smash Bros. for Wii U.

The Landmaster's appearance as Fox, Falco and Wolf's Final Smashes in Super Smash Bros. Brawl and Super Smash Bros. for Nintendo 3DS and Wii U is a composite of its appearances from Star Fox 64 and Star Fox Assault, maintaining the sharp and futuristic appearance it had in the latter, but still retaining traditional tank treads as seen in the former.

This particular design would eventually be implemented into the Star Fox series proper, beginning with the Landmaster's appearance in Star Fox 64 3D, and would be used again in Star Fox Zero.

The English manual and prologue for Star Fox Adventures implies a bigger backstory for Krystal, in that she's the sole remaining survivor of her doomed home planet, "Cerinia", and that she's been roaming the galaxy in search of answers for the truth of her family's death, until she receives a distress call from Dinosaur Planet. With how the manual states that Krystal "may finally be drawing closer to the truth" behind her parents' and planet's destruction, it seems Rare was loosely implying that Andross, who turns out to be the real villain of Star Fox Adventures and thus the culprit behind Dinosaur Planet's woes, was responsible for Cerinia's destruction. Krystal even says "It's you!" right before Andross imprisons her in the crystal at the top of Krazoa Palace.

However, it would seem the Japanese localization for Star Fox Adventures would completely eschew this backstory, removing all mention of Cerinia and as well as Krystal's dead parents. The Japanese prologue was even heavily simplified to this:


The Japanese website even states that "it is not known what her purpose is", which flies directly in the face of Rare's original story for her, that explicitly states that she was searching for the truth of Cerinia's destruction. To add more insult to injury, there isn't even any Japanese subtitle presented when Krystal gets knocked into the crystal by Andross in Krazoa Palace.

Curiously, the Japanese localization of Star Fox Adventures also heavily emphasizes Krystal having telepathic abilities, much more so than in the English version. This is noteworthy because neither Star Fox Assault or Star Fox Command, the next two story follows up to Star Fox Adventures that were developed and written in Japan, made any sort of mention of Cerinia. Star Fox Assault however would hugely emphasize her telepathic abilities, and its manual even describe Krystal the same way the Japanese version of Star Fox Adventures does, just as "a mysterious telepathic woman". This also applies to her trophies in Super Smash Bros. Brawl and Super Smash Bros. for Nintendo 3DS and Wii U that once again make no reference to Cerinia. It's very clear that the developers and writers behind Assault, Command and Smash Bros. in Japan were using the Japanese version of Star Fox Adventures as a reference, as opposed to the English version.

All in all, it would seem Nintendo of Japan had their own differing vision of what Krystal's character was from Rare, that being mostly just as a telepathic woman with a mysterious background, as opposed to Rare's original backstory of her being the lone survivor of her kind.

The official Japanese Star Fox 64 guidebook reveals that Pigma Dengar, who became a subordinate of Andross, was effectively the real mastermind behind the creation of Star Wolf: he goated and manipulated Wolf into becoming its leader and also working for Andross as a means to combat the newly formed Star Fox team led by Fox McCloud, taking advantage of Wolf's supposed honorable, "magnaimous" side and also his prior rivalry with Fox's father, James McCloud. It is said that he manipulates the entire team behind the scenes in accordance to Andross' orders. It also reveals that Pigma had already been working underneath Andross during his time as a researcher at the Corneria Defense Force Scientific Research Institute. It's also revealed that both Pigma and Andross had custom engineered the Wolfens that the Star Wolf team utilize in their battles against the Star Fox team's Arwings.

In Super Smash Bros. 4, the trophies for Pigma and the Wolfen would reiterate this information, as would the official guidebook for Star Fox Command. The Star Fox 64 Official Player's Guide would similarly allude to Pigma being the root cause of Fox and Wolf's rivalry, claiming that, without his influence, perhaps they could have been friends in another timeline.

Despite sharing a name, two different announcer takes were used for Roy from Fire Emblem and Roy from Mario, with the announcer using a sinister tone for the villainous Mario Roy and a prideful tone for the heroic Fire Emblem Roy.

As of Super Smash Bros. Ultimate in 2018, Shadow the Hedgehog is the only third-party Assist Trophy to appear in every Super Smash Bros. game since the introduction of Assist Trophies in Super Smash Bros. Brawl in 2008.

A potential stage based on Super Mario Land was considered for the Nintendo 3DS version to represent the Game Boy. However, a stage based on Kirby's Dream Land was used instead for unknown reasons (the stage was renamed to Dream Land GB in Super Smash Bros. Ultimate to avoid confusion with another stage already named Dream Land).

A reversal of this kind also happened in the Wii U version, where a stage based on Kirby's Epic Yarn was considered, but was revamped into a stage based on The Great Cave Offensive from Kirby Super Star after the development team heard about the then-upcoming Wii U game Yoshi's Woolly World.

While battle damage is used for Little Mac, data suggests that other characters were planned to have similar effects. This can be seen in unused textures for R.O.B. in the game's data which seem to show battle damage. This is a remnant from the development of Super Smash Bros. Brawl in which characters were also planned to have battle damage, but were left out.

The Pirate Ship stage from Super Smash Bros. Brawl was only included in the Wii U because of technical limitations of the 3DS.

Inside the game's files are unused gliding animations for Meta Knight, Pit, and Dark Pit. This may suggest that gliding was supposed to return from Brawl. However, it's likely that it was cut for balance reasons.