Author Existence Failure: In the Mexican Spanish dub, Leonardo's voice actor (Enrique Mederos) died in almost the beginning of the series and he's replaced by Luis Daniel Ramirez. The funniest thing in the recasting is Mederos voiced previously Fujitaka Kinomoto and Luis Daniel Ramirez voiced his son, Touya.
Bad Export for You: Inverted, Nickelodeon's release of Turtles Forever in the US is Pan and Scan rather than its original 16:9 widescreen, in addition they used the Edited for Syndication version which cut out at least one plot important scene and 8 minutes of footage altogether. The UK release averts this having the film in its entirety, in its original aspect ratio.
Given the inconsistencies in the way the series was distributed on DVD in the US, several bits are available only in inconvenient, out-of-print bits (season 3 and the first half of season 4), available in incomplete forms (Turtles Forever), or not available at all (Back to the Sewer).
Missing Episode: "Insane in the Membrane", which wasn't aired because Fox found it too intense for Saturday Morning cartoons. Also the entire fifth season was this, although it was eventually aired and billed as a series of "lost episodes".
The Other Darrin: Several characters eventually get recast, most notably Leatherhead (F.B. Owens to Gary Lewis).
What Could Have Been: The different rejected pitches for season 7 of the 2003 'toon, from Fast Forward season 2 to "Superworld". Concept art for these rejected series are now being released on 4Kids' ''TMNT'' blog. There's also "Nightmares Recycled", a season 5 episode that was planned but scrapped due to objections from standards and practices.
And apparently, had there been another Back to the Sewers season, they would have started a "Shredder Wars Arc", where it would answer how the fight between the Utrom, Demon, and Cyber Shredders got into their fight in the first place; this plan seemed to have been discarded in favor of Turtles Forever.
The "Nightmare Recycled" episode would have revealed that The Garbageman and Hun were born as conjoined twins, separated at birth by a seedy, back-alley surgeon; the baby that would later become Garbageman was thrown in the trash, whereas Hun was kept and raised. 4Kids, not surprisingly, felt that this was not for kids, and scrapped the episode before it could be completed.
Had a new season of Fast Forward emerged, there would have been a Triceraton Shredder called the "TriShreddertron". Concept art was eventually shown, and Peter Laird confirmed that he would have been Ch'rell taking over the body of a Triceraton soldier.
The three different pitches for the seventh season that were proposed before "Back to the Sewer" began production.
4Kids first pitched a season called "Superworld" which involved the Turtles playing some kind of card game.
After that pitch was rejected, 4Kids suggested "TMNT: Overload", which would have had the Turtles return to their own time after the events of Fast Forward, but have their younger selves come with them due to a glitch in the time travel process. Mirage approved of this development, but Playmates did not.
In lieu of "Overload", Playmates proposed a pitch for a Continuity Reboot called "Ultimate TMNT", which was planned to combine the 2003 universe with the continuity of the live-action films and feature characters from the 1987 cartoon and the Archie comic series. Eventually, "Ultimate TMNT" was rejected and "TMNT: Overload" was revised into what became "Back to the Sewer"