Creator Backlash: For your own safety, never, ever, ever mention this to franchise co-creator Peter Laird.
Executive Meddling: It is believed that Venus De Milo's creation was a result of this, though nothing was confirmed.
Not during the production of the show, but still related to it regardless. Peter Laird's hatred of this incarnation led to Venus De Milo not returning in the 2003 cartoon and all future incarnations that were under his rule. Only now is there even a possibility of such a thing happening.
Keep Circulating the Tapes: Nickelodeon owning the franchise, and Saban getting the rights back were probably the only reasons this show was finally able to release it in 2012 (at least, in America).
What Could Have Been: If the series had continued past the first season Splinter would have been Killed Off for Real (probably by the Dragonlord). Some fans think this dramatic development just might have been worth putting up with everything else.
Season 2 also apparently would have been animated and introduced April O' Neil and Casey Jones. The season finale also greatly hinted that The Shredder would have become the next season's Big Bad.
According to the book Teenage Mutant Ninja Turtles: The Ultimate Visual History, the fifth turtle Kirby from the scrapped fourth live-action film was supposed to be the fifth turtle in this series, but Saban refused to make the show unless the fifth turtle was female.