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.

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.

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.

A voice line of Snake saying "There!" can be found in the files for Super Smash Bros. Brawl. While it remains unused in this game, it would later be used for when Snake plants a C4 explosive in Super Smash Bros. Ultimate.

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.

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.

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.

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

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.

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.

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

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.

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).

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.

Tekken's Heihachi Mishima was briefly considered for the roster of Super Smash Bros. for Nintendo 3DS and Wii U, but was ultimately replaced with Ryu from Street Fighter. The team thought that implementing Heihachi's movement into the game would have been difficult due to fundamental design differences between the Tekken and Super Smash Bros. series, and instead released a Mii Fighter costume of him. He was once again considered for Super Smash Bros. Ultimate, but his son Kazuya was chosen instead due to him possessing the Devil Gene from his mother Kazumi. This choice was made to implement Kazuya's Devil Powers into midair jumps, smash attacks and special moves, while making the rest of Kazuya's moveset as similar as possible to his normal moveset in the Tekken series.