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.

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.

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.

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.

As of Super Smash Bros. Ultimate in 2018, only three characters that started out as Assist Trophies became playable in future installments:

•Little Mac, an Assist Trophy in Brawl, then became playable in Super Smash Bros. for 3DS/Wii U
•Dark Samus, an Assist Trophy in Super Smash Bros. for 3DS/Wii U, then became playable in Ultimate
•Isabelle, an Assist Trophy in Super Smash Bros. for 3DS/Wii U, then became playable in Ultimate.