Originally, Marge's megaphone had a limit on how many people she could recruit into her mob. In the final version, however, there is no limit, and she can recruit as many as she wants. In the game engine, her original upgrade would increase the number of mob members she could gather, rather than boosting her blowback strength as it does in the final game.

Originally, the level Game Over included a section where the player would use Lisa's Hand of Buddha to build a tower out of Springfield buildings and climb up to Heaven. This idea was eventually cut due to technical difficulties and time constraints.

According to producer Chuck Beaver, all of the game's FMV cutscenes were originally planned to be made in 3D using the in-game models. Late in development, Fox requested that they be changed to 2D animation in the style of the TV show, as they felt the 3D-to-2D approach didn't produce results that were "on-model". These 3D cutscenes still appear in the Nintendo DS version, though with some scenes, music, and sound effects removed, likely because they were unfinished.

The central shaft area in Enter the Cheatrix originally featured a giant drill bit that the player would climb by walking along its blades while fighting enemies. However, the developers found it difficult to get the collision and enemy pathing to work properly on a rotating object, so the idea was ultimately cut.

The level Around the World in 80 Bites was one of the first levels made for the game. According to level designer Jameson Durall, it was known internally as the "Core X" level, which was part of EA's greenlight process to decide whether the development of games would continue. The goal of this level was to prove that the team could deliver everything they had planned, making the game look like and maintain the humor of the original show, and implementing all the core mechanics. The team fully built out this single level so they could use it as a foundation and apply what they learned across the rest of the game.

There are two unused areas, called Zone 3 and Zone 4, for the level Enter the Cheatrix that still exist in the game files. According to level designer Ben Johnson, these areas were largely designed as filler, and were cut because they made the level feel too long. Zone 3 mostly repeated gameplay ideas from earlier areas, while Zone 4 was planned to be a combat segment with infinitely spawning enemies, where players would have to fight them while figuring out how to shut down the spawners.

Several level names were originally different during development:

• Lisa the Treehugger was originally called The Treehugger.
• Enter the Cheatrix was originally called Cheater, Cheater, Pumpkin Eater.
• Invasion of the Yokel-Snatchers was originally called The Day Springfield Stood Still.
• Five Characters in Search of an Author was originally called Rhymes with "Complaining".
• Game Over was originally called Meet Thy Player.

Despite the changes, the original names still remain in the game's code and file structure. Many of these early titles appear in early builds, and "Cheater Cheater" and "The Day Springfield Stood Still" were even reused for song names in the game's official soundtrack.

Originally, the Lard Lad boss fight in Shadow of the Colossal Donut was planned so that each hatch battle took place in a different area of the industrial zone, with the final fight happening inside the Duff Stadium. Notably, leftover voice lines and a subtitle text string for a scrapped in-game cutscene still exist in some early builds.

The New-Gen E3 2007 build of the Xbox 360 release revealed that the home console versions were originally meant to have cutscenes fully animated in 3D. A workprint containing these cutscenes shows a mix of finished and unfinished 3D renders and storyboards with placeholder voice acting, with the final game having cutscenes primarily animated in the same 2D digital animation as the show. The Nintendo DS version of the game is the only version that exclusively uses 3D cutscenes.

This build also reveals that the identity of the "sleazy video game producer" featured in Level 5: Mob Rules is Larry Probst, the former CEO of Electronic Arts from 1991-2007. The name is not fully censored in the DS version of the game, where Marge can be heard faintly saying his name under the censor tone in the level's opening cutscene. Probst's name also appears uncensored in the in-game cutscene for the level, where the dialogue is fully intact. In the final retail versions, the name is censored from the game's script when Mayor Quimby says it.

The game manual featured throughout every version's cutscenes (except the DS version) is the cover from the Xbox 360 version. The DS version, however, is actually from the in-game cutscenes used from every other version. Interestingly, the DS version’s cutscenes resemble the in-game ones from the other versions.

All "in-game" cutscenes from the Xbox 360 and PlayStation 3 versions were imported to the PlayStation Portable, Wii, and PlayStation 2 versions of the game despite obvious inconsistencies with the level designs.