Solid Snake's series logo was changed from the FOX emblem that was used in Super Smash Bros. Brawl, to the exclamation point seen when being caught in most Metal Gear Solid games.

This is likely because the FOX emblem (which first appeared in Metal Gear Solid 3: Snake Eater) is also commonly associated with series creator Hideo Kojima and his company Kojima Productions, a former subsidiary of Konami. Kojima left Konami in 2015 and the removal of the FOX emblem to represent the series is likely a biproduct of the split.

Super Smash Bros. Ultimate is the first game in the series that requires players to select a stage before selecting a character in multiplayer matches. In previous entries, as is common in other fighting games, it was the opposite. This is an attempt by Masahiro Sakurai to change up the strategy of the game (specifically stage-character match-ups).

According to Sakurai's Famitsu column, he chose to build the game off of the previous entry's mechanics instead of building the game from scratch as choosing the later would have caused a large portion of the game's roster to be cut. This would be due to the fact that more time would have had to be put into rebuilding each individual character.
He also remarked this decision allowed for more focus to be put on other aspects of the game.

Mirroring a similar easter egg on the Temple stage, the Sheikah text on a platform in the Great Plateau Tower stage says "SMASHBROS" twice.

When Pit gets Star KO'd, he'll shout out that he never learned how to read. This is likely a reference to a scene from Kid Icarus: Uprising Spoiler:when Palutena cuts off his power of flight upon defeating Pyrrhon.

Yoshi's new Final Smash, where he summons an army of multi-colored Yoshis, is a reference to his part in the opening of Super Smash Bros. Melee.

Ridley's orange palette swap is in reference to the villain's appearance on the box art of Super Metroid.

Unlike other boss characters, Spoiler:Giga Bowser is classified as a fighter in the game's files, even having placeholder slots for alternate costumes.

These are likely leftovers from the previous game, Spoiler:where Giga Bowser appeared as a playable transformation.

Files for Dragonite from the Pokémon series suggest it may have been planned to be summoned from the Poké Ball. While it does not appear as an assist character in the final game, it does appear as a background character in the Kalos Pokémon League stage. Two models for the character exist, with one more in line of those summoned by the player, featuring higher resolution textures.

Taking the camera inside of Dungeon Man on the Magicant stage will allow you to see Brickroad, who was the operator of the man-dungeon hybrid in EarthBound.

The voice clip used for when Snake plants a C4 is a clip that originally went unused in Super Smash Bros. Brawl.

It was thought to have originally served the same purpose as it does in Ultimate.

If one hacks the camera in the recreated Great Bay stage from Melee and points it to the far left, it's possible to see geographically accurate landmarks originally seen in the world of Termina from The Legend of Zelda: Majora's Mask that aren't seen during normal gameplay.

This includes a series of ledges leading to an alcove with a Heart Container inside of it, Fisherman's Island, and the large gated entrance to the Pirate's Fortress, complete with a new design featuring two crossed swords.

These do not appear at all in Melee.

Charizard, Incineroar, the Inklings, and Sonic the Hedgehog are the only characters that take continuous damage when in water. This is in reference to their respective series, as Sonic cannot swim, Inklings are instantly killed when they come in contact with water, Incineroar and Charizard are fire-type Pokémon which are weak against Water-based attacks.

According to Masahiro Sakurai, in an interview with Famitsu, the reason why Kirby (being a creation of Sakurai's) was the only one that survived Galeem's attack was because he was the only one who could plausibly escape it using his Warp Star. This also made the character accessible to starters or newcomers to the game, as a result of his speed and attacks.

Many of the unique titles for each fighter in Classic Mode contain Easter eggs and references. A few examples are:
*Mario's title "Let's-a-Go" is a reference to one of his phrases.
*Link's title "A Quest to Save Darkness" references the plot of most Zelda games where he's on a mission to seal Ganon away.
*Dark Samus' title "The Great Poison Given Form" references the essence she was created from in the Metroid Prime series.
*Kirby's title "Gourmet Clash" references the Gourmet Race minigame from Kirby Super Star.
*Pikachu's title "I Choose You!" is based off Ash Ketchum's signature catchphrase from the Pokemon Anime, as well as the name of the Anime's first episode.
*Luigi's title "Luigi's Nightmare" is likely a reference to his cowardly personality.
*Ness' title "Home to Onett" is a reference to the Homesick status featured in Earthbound.
*Jigglypuff's title "All Original, All 64" is a reference to the fact that Jigglypuff is a member of the Perfect Attendance Crew for being in every Super Smash Bros. game since the original for the Nintendo 64, and the opponents it faces are against other members of the Perfect Attendance Crew.

Abby Trott, the vocalist of the English version of Lifelight, stated in a interview that she actually cried upon hearing that she would be involved in "Super Smash Bros. Ultimate." Trott, herself, was a Nintendo fan and hearing about this made her feel "very special."

“I was lucky enough to have the opportunity to audition through Cup of Tea Productions, and at the time I had no idea what the audition was for. For the first round, I submitted my singing demo. The second round involved singing a requested song (not ‘Lifelight’). I ended up being cast, and CRIED when I found out what the project was. As a life-long fan of Nintendo, being a part of Smash Bros. Ultimate is really special to me. I love ‘Lifelight’ so much.”

Jun Senoue, famous for being a lead music composer for Sonic Adventure 1 and 2, said he was insipired to write and arrange Super Smash Bros. Ultimate's "Mega Man 4 Medley" in the style of a Sonic Series composition after he came across a Sonic and Mega Man crossover comic that sparked his imagination. He chose to center his arrangement on the 4th Mega Man game because of fond memories that he had of playing the game at university.

The plot of the Adventure Mode: World of Light, in which Kirby is the sole survivor of a cataclysmic invasion and must rescue the other fighters, was actually series director Masahiro Sakurai's original vision for the plot of Super Smash Bros. Brawl's Adventure Mode: The Subspace Emissary.

This early storyline was mentioned during a 2008 Iwata Asks interview:
"I had envisioned a more serious tone for the story. Something with some misfortune like a single character escaping total annihilation of his squadron and then fighting back while rounding up his allies."

It should be noted however that Spoiler:this early storyline would be implemented somewhat closer to the end of The Subspace Emissary anyway when Tabuu decimates every fighter turning them back into trophies, while Kirby, Luigi and Ness are revived in separate locations thanks to the three Dedede Brooches.

When Piranha Plant was revealed as the first DLC character, many fans were bewildered, as a generic enemy has never been a playable character in the Super Smash Bros. series before. Despite this, in an interview with Game Informer, Masahiro Sakurai has stated that he never intended to surprise people with the Piranha Plant, and that it was a character everybody would know of.

Although Terry Bogard from Fatal Fury had made it into the game as a downloadable character, Masahiro Sakurai had initially planned to add Mai Shiranui alongside Terry. In the Japanese Nintendo Direct presentation of Terry Bogard, he explained further that he worried that CERO (Japan's video game rating board) would raise the rating from A (for all Ages) to a higher one which was why he reconsidered having her in the game, joking that Super Smash Bros. was only for "good boys and girls".