When Prince Florian was first revealed in the June 2023 Nintendo Direct for the game, some fans believed that he was either a callback or reimagining of Prince Haru, a character that only appeared in the 1986 anime film "Super Mario Bros: The Great Mission to Rescue Princess Peach" who transforms from a dog known as Kibidango into a human. This prospect was seen as troubling by Mario fans who partake in shipping, with some believing that Mario and Peach would be retconned as no longer being romantically interested, with Florian taking Mario's place as Peach's boyfriend, as Haru was in the movie.

Upon the game's release, Florian would not show any romantic interest in Peach, nor transform into a human, with their only similarities being that they are princes of flower kingdoms and Florian's facial structure baring a loose resemblance to that of Kibidango.

Two "Break Time" stages in Sunbaked Desert prominently incorporate music from Super Mario Sunshine: the level "Break Time! Raise The Stage" uses the track "Secret Course", while "Break Time! Bouncy Tunes" uses the track "Isle Delfino" (commonly known as the Delfino Plaza theme).

The use of music from Super Mario Sunshine appears to tie in with the subplot for Sunbaked Desert, in which Bowser Jr. hoards the region's water for himself; Sunshine was previously a water-themed game featuring Bowser Jr. as the main antagonist.

One scrapped idea for a Wonder Flower transformation was an eight-heads-tall, life-size, live-action version of Mario that hummed to the background music and exclaimed "Boing" when jumping. This idea was pitched by series composer Koji Kondo, but was scrapped due to it being "hard to see the connection between pre-Wonder effect and during Wonder effect. And it's hard to imagine the gameplay changing much by having Mario turn into a live-action, human proportion version of himself." However, this did end up leading to the Sound Off? badge being created to keep the voice sound effects idea in the game. Incidentally, Kondo provided the voice acting for all of the sound effects included while wearing the badge.

In an interview conducted for Nintendo's Ask the Developers blog, designer Koichi Hayashida revealed that producer Takashi Tezuka wanted to implement a live commentary system that would remark on the player's actions and progress, similar to a sports newscaster. Programming director Shiro Mouri elaborated that the idea polarized the development team, who were "evenly split between those in favor and those against," and that the mechanic would've allowed the player to toggle between a standard newscaster voice and a tsundere voice (i.e. a voice which treats the player coldly on the surface but hints at a hidden affection towards them), the latter of which was unexpectedly popular with playtesters.

According to Tezuka, the idea was eventually scrapped due to the impracticality of it, as the mechanic would've required a large amount of work to create different voice variations and have them dynamically respond to the player. Instead, the concept was reconfigured into the Talking Flowers, which Mouri described as "a version of live commentary that fits the world of Mario."

According to Super Mario Bros. Wonder's art director Masanobu Sato, Shigeru Miyamoto reportedly explained during the development of the first Super Mario Bros. that the reason why Goombas damage Mario when walking into them is because they bite Mario on impact. Due to graphical and hardware limitations, this could not be shown at the time. However, while Super Mario Bros. Wonder is thought to be the first game in the mainline series that shows this detail in gameplay, it's not the first game in the overall franchise to show it, as Goombas had been seen biting in earlier spin-off games like Super Mario RPG: Legend of the Seven Stars.

An idea for Elephant Mario once involved inflating a Koopa Troopa shell thus allowing Mario and friends to carry it around with them. The idea got shot down after developers had trouble knowing what to do with them. A remnant of the idea still exists in-game, allowing Elephant Mario to carry large objects that are already on the stage.

The idea for making the Mario characters and enemies more expressive in Super Mario Bros. Wonder than in previous games (including the New Super Mario Bros. franchise) came during an early part of development. Masanobu Sato stated, in an Ask the Developer interview with Nintendo, that they wanted to "implement more engaging and functional ways of using 3D models in this 2D platformer."

Looking back at the New Super Mario Bros. games, Sato recalled that "It's a well-known story within the company [Nintendo] that Miyamoto-san said designing Mario's nose to be big back in the day of the very first pixelated Mario made it easier to see which direction Mario was facing. But if we set Mario's nose to face the direction of travel, like we used to, with a modern 3D model, you wouldn't be able to see his facial expressions."

In an Ask the Developer interview by Nintendo, Takashi Tezuka said that the need for a new side-scrolling platformer came out of necessity from him. According to Tezuka, many journalists and players felt that the Super Mario Maker franchise would have ended the need for another 2D Mario game. Tezuka, however, always felt confident that Wonder would be completely different from other side-scrolling Mario installments.

Coming up with brand new ideas was a challenge for Tezuka and his then-small team, and resulted in over 2,000 different ideas on how to make Wonder look fresh and out-of-the-box.

Super Mario Bros. Wonder is the first Mario game to feature Kevin Afghani as the voice of both Mario and Luigi, replacing Charles Martinet, who announced his retirement from voice acting and shift to a brand ambassador position earlier in 2023.

While Afghani didn't announce his involvement until October 13, 2023, his presence in the game was leaked two days earlier on 4chan, when an anonymous user datamined a kiosk demo and leaked the game's voice cast, backing this up with images showing parts of the game that hadn't been publicly revealed yet. Because the cast list didn't state the voice actors' roles, users used process of elimination to determine who Mario's voice actor was, incorrectly guessing that it was Mick Wingert after assuming that Afghani was only voicing the Talking Flowers. In a statement sent to IGN, Wingert's agent refuted the claim that he was voicing Mario, and was later revealed to actually be the voice for the Talking Flowers.

The Elephant Fruit power up is possibly based on a real world fruit known as "Dillenia indica", commonly nicknamed the Elephant Apple, which the power up is called in the Dutch, French and Portugese translations of the game.

In an interview with IGN, the game's director Shiro Mouri said that Mario's creator Shigeru Miyamoto was, at first, not a fan of Elephant Mario as he believed it "did not look like a Mario character." Miyamoto also believed the physics for the power-up wasn't realistic to an actual elephant. The popularity with fans after its reveal was what eventually changed Miyamoto's mind.

In the game's Japanese reveal trailer, Wonder Seed was spelled as "Wonderseed".

The idea for the Wonder Flower came from an effort to introduce surprising elements that would challenge the player. Originally, the idea was to introduce items that would warp players to a new area, but the game's producer Takashi Tezuka didn't find it interesting, saying: "If you're still just going to warp to a different area, it's still the same. Why don’t you just change where you are right now?"

This game marks the first time that Princess Daisy is playable in a mainline Mario game on a Nintendo console after her first playable appearance in the mobile game Super Mario Run. According to Super Mario Bros. Wonder's director Shiro Mouri in a 2023 interview with Eurogamer, Daisy's inclusion was spurred from a personal family anecdote:

Super Mario Bros. Wonder marks the first game to not feature performances from long-time voice actor Charles Martinet, who voiced Mario and Luigi (and Wario and Waluigi in other games in the series) since 1990.

Nintendo announced that Martinet would retire from portraying the Mario Bros. permanently and become a "Mario Ambassador", nearly two months before the game's release.