Approval of God: In contrast to Peter Laird, the other franchise's co-creator Kevin Eastman actually likes Venus de Milo as a character and even hopes that she can make a comeback someday now that the franchise is out of Laird's hands.
Creator Backlash: To say that franchise co-creator Peter Laird didn't think highly of this series would be a huge understatement. He especially loathed Venus de Milo to the point that he forbade her from ever being so much as mentioned in any other continuity for the duration that the franchise was in his hands. Many believed that the same held true for the franchise's other co-creator Kevin Eastman, but the trope above proves otherwise.
It was believed that Venus De Milo's creation was a result of this, though it wasn't confirmed until this interview with Kevin Eastman, where he stated that Venus was supposed to be the fifth turtle Kirby from the scrapped fourth live-action film, but was made female at the insistence of Fox Network head Margaret Loesch.
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. In fact, even mentioning her was forbidden outside franchise retrospectives and history books. Only now is there even a possibility of such a thing happening due to the franchise now being out of Laird's hands.
Exiled from Continuity: Due to Peter Laird's immense hatred of Venus, he did not allow her to make an appearance or even be referenced in other Ninja Turtles continuities. The Next Mutation didn't even show up in the multiverse scene in Turtles Forever, although this one might have been more about The Next Mutation being owned by a different company.
God Never Said That: While Peter Laird's hatred of Venus de Milo is rather well-known, many fans who disliked the character mistakenly believed that the franchise's other co-creator Kevin Eastman had the same opinion on Venus. An interview with Eastman after Nickeldoeon obtained the rights to the franchise, however, proved that Kevin likes Venus and hopes for her to make a comeback someday.
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 be released on DVD in 2012 (at least, in America).
Role Reprisal: Matt Hill returns as the voice of Raphael from Turtles III.
Show Accuracy/Toy Accuracy: Splinter has brown fur and, as in the live-action films, has one of his ears slashed off, but his action figure in the show's toyline gives him grayish fur and has both of his ears intact.
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.