Contrary to popular belief, there is evidence suggesting that Super Mario Bros. 2 was the true sequel to Super Mario Bros. Some time after the original game's completion, Nintendo's Kyoto-based R&D division began working on a vertical-scrolling Mario engine. It became clear early on that a vertical-scrolling game couldn't offer the same quality of platforming as the original Super Mario Bros. Shigeru Miyamoto then stepped in and added horizontally scrolling aspects to the game.

The prototype engine was originally designed around carrying, throwing, and piling up items and featured 2-player cooperative play, which even included the ability to throw other players to hard-to-reach places to progress further in the game. A deal with Fuji Television was struck during development to promote their 1987 Japanese festival the Communication Carnival Yume Kōjō '87 (translated to English as "Dream Factory '87"), and the prototype eventually became Yume Kōjō: Doki Doki Panic. Although cooperative play was dropped, the concepts of vertical scrolling and tossing around items to defeat enemies was incorporated into Doki Doki Panic, and in turn Super Mario Bros. 2. All of this supports the thought that Super Mario Bros. 2 was, in fact, the true sequel.

As of 2023, only 4 licensed IP adapted games have been released on Nintendo's retro game digital download services: Teenage Mutant Ninja Turtles for NES on Wii (which was later delisted on January 26, 2012), Transformers: Mystery of Convoy for NES on Wii, Quest for Camelot for Game Boy Color and GoldenEye 007 for N64, the latter two being on Switch.

Additionally, J.J. & Jeff, Punch-Out!! Featuring Mr. Dream, and Super Mario Bros. 2, all reskins of licensed titles, have been available in their license-less formats.

World 7 of Super Mario Bros. 2 (and in turn the original Doki-Doki Panic) only has 2 stages instead of the standard 3 used for stages in the rest of the game. This is due to the plotline in the manual of the original Doki-Doki Panic, where the final page of the book the twins were teleported into was torn out. This detail was not given an equivalent in Super Mario Bros. 2's plotline, and even in the original Japanese release was not mentioned in-game, and as such could come off as an oddity to players of the original version too should they not read the manual.

When Birdo (known in Japanese as Catherine) was first introduced in Yume Koujou: Doki-doki Panic, the game's manual gave this description:


This carried over to the manual for the game's Western reskin as Super Mario Bros. 2 (known as Super Mario USA in Japan), where it instead states that Birdo's preferred name is "Birdetta". Starting with the commercial for Super Mario USA, Birdo was depicted in Japanese media as a flamboyant and flirtatious okama (a Japanese-language derogatory slur used to refer to gay men, transgender women, male crossdressers, and/or effeminate men) in both her voice acting and mannerisms for comedic purposes. However, this depiction, as well as the Western Birdetta name, were largely omitted from English localizations of future Mario games, with some exceptions:

• Mario & Luigi: Superstar Saga, where Birdo appears as an accomplice of Popple, who feels confused and discomforted by her.
• Super Smash Bros. Brawl, where Birdo's trophy description calls Birdo "gender indeterminate", uses "it" instead of a gendered pronoun, and includes the omitted Birdetta name.
• Super Mario Party, where Birdo is referred to with she/her pronouns in the American English script, he/him pronouns in the British English script, and no gendered pronouns in the Japanese script.

Birdo's Japanese depictions drew characteristics from drag queens and transgender women in Japanese pop culture, and Birdo would retain toned down elements of these in subsequent reappearances. Birdo frequently refers to herself in Japanese media with both the first-person feminine pronoun "atashi" and the gender-neutral first-person pronoun "watashi", invoking the latter in a feminine manner. In the Satellaview game BS Super Mario USA, the three types of Birdo are voiced by Shiroi Heya nightclub performers Jun Donna, Rika, and Akemi, all of whom identified as newhalves (a Japanese term interchangeably used to refer to transgender people and male crossdressers). Birdo's gender is most explicitly addressed in Captain Rainbow, where she is depicted again as an okama and is arrested for using a women's restroom. This forms the basis for a sidequest where she can only be exonerated once the player finds a censored item in her house called the "female proof" that is strongly implied to be a vibrator. In one trailer for the game, Little Mac describes Birdo as a "young lady", before pausing and restating: "Depending on one's view point, she is a young lady."

In 2015, a representative for Nintendo told the Japanese news site Netorabo that Birdo, as well as Yoshi, were neither male or female, or even dinosaurs; Birdo was "someone who believes they are a girl [...] 'Yoshi' is 'Yoshi' and 'Catherine' is 'Catherine'".

Super Mario Bros. 2 was technically not a unique Mario game, but rather an enhanced port of a Japanese game called "Yume Kōjō: Doki Doki Panic", translated to English as "Dream Factory: Heart-Pounding Panic". The "Dream Factory" part of the name refers to an expensive 1987 Japanese expo organized by Fuji Television called the Communication Carnival Yume Kōjō '87 that showcased various upcoming programs. As part of an ongoing license cooperation between Nintendo and Fuji, the festival's four main mascots became the playable characters in the game, while all other characters were created by Nintendo. It was ported and released in North America with Mario, Luigi, Princess Toadstool and Toad replacing the mascots. This was released in place of the Japanese Super Mario Bros. 2 (known in the US as Super Mario Bros.: The Lost Levels) because Nintendo of America considered it to be too difficult and too similar to the first Super Mario Bros. to compete with rapidly advancing games from rival companies.