The game was originally an arcade game titled The Fast and the Furious, which was soon ported to the Wii with any references to The Fast and the Furious being removed entirely due to Midway losing the license to the series during the game's development.
The game was going to have an extensive training mode where players are taught the mechanics of the game--from simple weapon clashes all the way up to death combos. The mode was ultimately left out from the final game due to memory limitations and time constraints.
The game was originally going to have a story mode which took place after the events narrated in arcade mode, but it was ultimately left out from the final game.
The ability to strip the clothing of certain humans was originally intended to be used for a side mission for Military Mayhem. The side mission in particular would've involved Zephyr pantsing the wandering soldiers in the first zone of the level.
By swapping map files, it is possible to play the first two single-player exclusive levels in co-op mode. The first level, Roadside Destruction, plays like a regular co-op level while the second level, Chicken Con Carnage, requires player one to take control of the tornado while the second player grabs the Fire Flyers. This mechanic was eventually reused during the Vortex Race and Totem Battle segments after completing all zones.

An E3 2009 developer walkthrough revealed that the game had a removed mechanic called advance chain collecting, which completely removes the smoke, sparks, and sizzling sounds emitted from objects containing Fire Flyers. As a result, this changes the game's difficulty. It is possible to enable this mode in the Wii version of the game via modding.
In 2019, a tutorial video was recovered from a deleted hard drive. The tutorial video included a powerup known as the Fujita Frenzy that allows the tornado to instantly grow in size and destroy larger buildings.
According to the developer's texts left in the Xbox 360 and PlayStation 3 versions' data, Nelson Muntz was originally going to be the boss of the NeverQuest level as a troll, instead of the two-headed Patty & Selma dragon.
In the code for the "Alien Auto-topsy: Part 1" mission, there is a command called "AllowRockOut()" which can be triggered after collecting the nuclear waste barrel and parking the car while Homer is a passenger and someone else is driving (this can be performed while Homer is the driver, but is reportedly trickier to pull off). Homer can then be seen "rocking out" to the mission's music by performing the "Task Completed" animation over and over again (any other character animations will temporarily override it). However, if you cancel the mission during this animation loop, it will be revealed that the speed he rocks out at changes to accompany the tempo of the song that is currently playing. The RMS files (which control music events) contain tempo data for every song in the game, despite mission warping effectively causing rocking out to go unused.
There is an unused Splitscreen mode in the game's data that seems to imply that the Story Mode was going to support Local Co-op instead of just the Online Co-op it supports in the final release.

According to Yuichiro Hiraki, the game was originally going to feature quick time events. Their implementation was scrapped due to mostly time constraints. Hideki Kamiya had a specification document that had a storyboard detailing an action sequence between Dante and a Blade.
"There were going to be a bunch of OTEs, like when Dante just barely dodges the pursuing Phantom. But we were... a bit frazzled at the time. so we begged and pleaded to have no QTEs. (laughs) That was just one gameplay element that was never realized. mostly because of time constraints."
"There were going to be a bunch of OTEs, like when Dante just barely dodges the pursuing Phantom. But we were... a bit frazzled at the time. so we begged and pleaded to have no QTEs. (laughs) That was just one gameplay element that was never realized. mostly because of time constraints."

Within the data for Chapter 2 is an unused attack for Spoiler:Spamton NEO in which the player is limited to shifting the SOUL between three horizontal planes while dodging oncoming oversized bullets. This attack functions identically to the Purple SOUL mechanic in Undertale, implying that at one point, Spoiler:the Spamton NEO fight was intended to be based around that rather than the Yellow SOUL mechanic.
Within the data for Chapter 1 is an unused attack for Spoiler:Jevil that consists of multiple spades converging into the center of the Bullet Board in a cross pattern. This attack would eventually be repurposed for the rematch against Berdly in Cyber City during Chapter 2, albeit with tornados in place of spades.

In typical gameplay, Spoiler:the UFO room in Queen's mansion is locked off during the Weird Route in Chapter 2. However, it still remains in the game's code, and modifying the game to access it reveals that Spoiler:the UFO hazards are replaced with the plug hazards seen both near the start of the Cyber Field and near the end of the mansion.
In a Famitsu interview Sakurai revealed that he and his team wanted to introduce aerial Smash Attacks in this game in order to diversify the limited aerial combat of Smash Bros. However, they rejected this for various reasons, including the belief that such attacks were "too complicated" to implement and also that, in Sakurai's opinion, the system would also destroy the game and series' signature balance between casual and competitive gameplay.
There are unused pieces of data and strings in the game that suggest a 2-Player local VS. mode was planned that didn't end up in the retail release of the game.
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