The 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 whose name was censored from the script in the final game.

Gameplay of a prototype version from 2004 was uploaded to YouTube. The player controls only Bart Simpson and runs around in the house. The game was played on the original Xbox, suggesting such an OG Xbox version may have been planned at one point.

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.

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.

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.

The Zero Wing parody image in Invasion of the Yokel-Snatchers was originally going to be a Simpsonized version of CATS, rather than Kang and Kodos dressed as CATS.