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 in non-anamorphic widescreen note meaning that while the movie is letterboxed, if watched on a widescreen TV, the black bars would still be intact, listed as full screen. 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, being enhanced for widescreen televisions.
Creator Backlash: Inverted. Peter Laird, who helped develop the show, said that he didn't like Hun that much at first. As the series went on, Hun ended up one of his favorite characters, to the point that he made his way into the comic books. Played straight with Baxter's mutilation, however, saying he never particularly liked that approach, although he agreed that Baxter's eventual fate was fitting.
Executive Meddling: As mentioned on the introduction, the 5th season got skipped in favor of the Fast Forward season. This caused the 4th season to end in a cliffhanger for some time.
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).
Some light at the end of the tunnel is finally starting to shine however, as Nicktoons Network has announced that they will start airing episodes of the 2003 series. Whether this means that the episodes will get new DVDs remains a mystery, but at least the series will be able to be viewed on television again.
Paramount and Nickelodeon have started releasing DVDs - unfortunately, they only contain three episodes each, and only collect random episodes and arcs.
The Other Darrin: Several characters eventually get recast, most notably Leatherhead (F.B. Owens to Gary Lewis).
Screwed by the Lawyers: Nickelodeon's acquisition of the Teenage Mutant Ninja Turtles franchise from Mirage Comics caused 4Kids to pull the plug on this series. Nickelodeon would create their ownTMNT in its place.
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.
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"
Peter Laird's blog shows off emails between him and other writers, with him critiquing or suggesting tweaks to the scripts.
On his blog, Peter Laird suggested that "Reflections" be about April writing into her journal, which would have eventually gotten lost and into the hands of a passerby, who would be interested in turning it into a comic book.
The underground genetics lab from "Notes from the Underground" was suggested as a hideout for the Shredder, but Laird said that would put him too close to the Turtles and they didn't want to rehash too many of Season 1's locations.
Nano almost stayed with the Turtles, but Laird wasn't comfortable with the idea so he suggested to wrap up Nano's story with "The Return of Nano" (at least until he was brought back for Season 5).
The Shredder originally planned to destroy the Earth with a bomb as he left in Exodus, but it was scrapped for it being too out-of-character for him and everyone else around him.
The series was pitched in 2001 and was considered to be aired on either Cartoon Network or the WB Network with a much less realistic art style (the Turtles looked much closer to the original art style of the comics, in particular), but WB scrapped it.